Cytochrome P450RAI-2 and related proteins

ABSTRACT

The present invention provides a novel all-trans-RA inducible all-trans-RA metabolizing cytochrome P450, P450RAI-2, that is predominantly expressed in the brain, cerebellum in particular. Human P450RAI-2 show 42% amino acid identity to human P450RAI-1 and when transfected into COS-1 cells causes the rapid conversion of all-trans-RA into more polar metabolites including the inactive products 4-oxo-RA, 4-OH-RA and 18-OH-RA. P450RAI-2, as with P450RAI-1, is also inducible in certain cultured cell lines exposed to all-trans-RA. Methods for and uses of the new polynucleotide, polypeptide, fragments thereof and inhibitors thereof, include the treatment of dermatological disorders and cancer.

PRIOR APPLICATIONS

This application claims priority from U.S. Provisional PatentApplication No. 60/171,110 filed Dec. 16, 1999 and U.S. ProvisionalPatent Application No. 60/178,314, filed Jan. 27, 2000 both of which areincorporated herein by reference.

FIELD OF THE INVENTION

The present invention relates to a novel gene encoding a polypeptidethat is a member of the cytochrome P450 family. More particularly thepresent invention relates to a polynucleotide encoding the novelpolypeptide, to an antisense polynucleotide thereof and to fragmentsthereof. The invention further relates to the novel cytochrome P450 aswell as to vectors, host cells and antibodies to the polypeptide and therecombinant methods for producing the same. Uses and methods relating toany of the foregoing are also included within the scope of theinvention.

BACKGROUND OF THE INVENTION

Cytochrome P450s

The cytochromes P450 comprise a large gene superfamily that encodes over500 distinct heme-thiolate proteins that catalyze the oxidation of drugsand numerous other compounds in the body [Nelson et al., (1996);Guengerich (1991)]. Since there are at least 500 different cytochromeP450 enzymes, it is of considerable interest in the pharmaceutical andother fields to identify which of these enzymes are most important inthe metabolism of individual compounds. There are now numerous examplesof adverse drug-drug interactions and side effects that can now beunderstood in terms of the cytochrome P450 enzymes.

P450 proteins are ubiquitous in living organisms, and have beenidentified in bacteria, yeast, plants and animals [Nelson et al (1996);and Nelson, (1999a)]. The P450 enzymes catalyze the metabolism of a widevariety of drugs, xenobiotics carcinogens, mutagens, and pesticides, andare responsible for the bioactivation of numerous endogenous compoundsincluding steroids, prostaglandins, bile acids and fatty acids body[Nelson et al., (1996); Guengerich (1991); Nebert et al., (1989)].

Cytochrome P450 metabolism of xenobiotics can result in detoxificationof toxic compounds by their conjugation into excretable forms or canresult in activation of compounds into metabolites that are toxic,mutagenic, or carcinogenic. Many steroids are deactivated by cytochromeP450-catalyzed oxidation.

Vitamin A and Retinoic Acid

Vitamin A metabolism gives rise to several active forms of retinoic acid(RA) which are involved in regulating gene expression duringdevelopment, regeneration, and in the growth and differentiation ofepithelial tissues. [Maden, 1992; Chambon, 1995; Mangelsdorf, 1995;Gudas, 1994; Lotan, 1995; Morriss-Kay, 1996] RA has been linked toapoptosis, or programmed cell death in a number of cell types; and tohave anticarcinogenic and antitumoral properties [Lotan, 1996].

Early studies of retinol deficiency indicated a correlation betweenvitamin A depletion and a higher incidence of cancer and increasedsusceptibility to chemical carcinogenesis [Chytil, 1984]. Several animalmodels have been used to demonstrate the effectiveness of retinoids insuppressing carcinogenesis in a variety of tissues including skin,mammary epithelia, oral cavity, aerodigestive tract, liver, bladder andprostate [Moon, 1994]. These studies have led to the preventative use ofretinoids to treat premalignant lesions including actinic keratosis andoral leukoplakia, as well as in the prevention of secondary tumors ofthe head and neck and the recurrence of non-small cell lung carcinomas,and basal cell carcinomas [Hong, 1994; Lippman, 1995]. RA itself hasbeen found to be useful therapeutically, notably in the treatment ofcancers, including acute promyelocytic leukemia (APL), tumors of thehead and neck, and skin cancer, as well as in the treatment of skindisorders such as the premalignancy associated actinic keratoses, acne,psoriasis and ichthyosis. There is evidence that the effectiveness of RAas an anti-tumor agent is at least partially due to induction ofcellular differentiation and/or inhibition of proliferation [Lotan,1996]. Studies over the past several years indicate that a highproportion of patients with acute promyelocytic leukemia (APL) achievecomplete remission after a short period of treatment with all-trans RA.Unfortunately, this high rate of remission is in most cases brief.Following relapse, patients are clinically resistant to furthertreatment with RA [Warrell, 1994; Warrell, et al., 1994; Chomienne,1996; Muindi, 1992]. The nature of this resistance is unknown.Interestingly, leukemic cells taken from patients exhibiting clinicalresistance to RA have been shown to be sensitive to the differentiatingaction of RA when grown in vitro [Muindi, 1992; Muindi, 1994]. Thissuggests that pharmacokinetic mechanisms may account for the acquiredresistance to RA. This possibility is supported by studies showing thatpeak plasma concentrations of RA were much higher in patients afterinitial administration than in patients treated following relapse. Thisdecrease in peak plasma RA concentration was accompanied by a 10-foldincrease in urinary 4-oxo-retinoic acid concentration. In addition,ketoconazole, a broad spectrum inhibitor of cytochrome P450 function wasshown to modulate RA pharmacokinetics in vivo [Muindi, 1992; Muindi,1994]. It is therefore likely that RA increases the rate of its ownmetabolism which in turn results in the inability to sustain effectivetherapeutic doses of RA. Therapeutic administration of RA can result ina variety of undesirable side effects and it is therefore important toestablish and maintain the minimal requisite doses of RA in treatment.For example, RA treatments during pregnancy can lead to severeteratogenic effects on the fetus. Adverse reactions to RA treatment alsoinclude headache, nausea, chelitis, facial dermatitis, conjunctivitis,and dryness of nasal mucosa. Prolonged exposure to RA can cause majorelevations in serum triglycerides and can lead to severe abnormalitiesof liver function, including hepatomegaly, cirrhosis and portalhypertension.

RA metabolism may also account for the lack of response of certaintumors to RA treatment. For example, recent studies have shown thatcytochrome P450 inhibitors that block RA metabolism, resulting inincreased tissue levels of RA, may be useful therapeutic agents in thetreatment of prostate cancer [Wouters, 1992; De Coster, 1996]. Thus RAmetabolizing cytochrome P450s may be useful targets for the treatment ofa number of different types of cancer.

The classical view of vitamin A metabolism holds that all trans-RA, themost active metabolite is derived from conversion of retinol toretinaldehyde to RA through two oxidation steps and that RA is furthermetabolized to the polar derivatives 4-OH RA and 4-oxo RA [Blaner, 1994;Napoli, 1995; Formelli, 1996; Napoli, 1996]. It is unknown whether the4-oxo- and 4-OH- metabolites are simply intermediates in the RAcatabolic pathway or whether they can also have specific activitieswhich differ from those of all-trans RA and 9-cis RA. Pijnappel et al.[Pijnappel, 1993] have shown that, in Xenopus, 4-oxo-RA can efficientlymodulate positional specification in early embryos and exhibits a morepotent ability to regulate Hoxb-9 and Hoxb-4 gene expression thanall-trans RA. 4-oxo-RA has been found to bind to retinoic acidreceptor-β (RAR-β) with affinity comparable to all-trans RA [Pijnappel,1993] but poorly to RAR-γ [Reddy, 1992], suggesting that this metaboliteexhibits some receptor selectivity. 4-oxo-RA also binds to cellularretinoic acid binding protein (CRABP) but with an affinity slightlylower than that of all-trans RA [Fiorella, 1993]. Takatsuka et al.[Takatsuka, 1996] have shown that growth inhibitory effects of RAcorrelate with RA metabolic activity but it is unknown whether there isa causal relationship between production of RA metabolites and growthinhibition. The asymmetric distribution of these metabolites indeveloping embryos suggests that they may be preferentially sequesteredor generated by tissue specific isomerases [Creech Kraft, 1994]. Thenormal balance of these metabolites is dependent upon rate of formationfrom metabolic precursors, retinol and retinaldehyde [Leo, 1989], andrate of catabolism. Little is presently known about the enzymes involvedin this metabolic scheme, in particular the catabolism of RA.

The catabolism of RA is thought to be initiated by hydroxylation eitherat the C4-, or C18-position of the β-ionone ring of RA [Napoli, 1996].The C4-hydroxylation step is mediated by cytochrome P450 activity, asjudged by the ability of broad spectrum P450 inhibitors such asketoconazole and liarazole to block 4-hydroxylation [Williams, 1987, VanWauwe, 1988; Van Wauwe, 1990, Van Wauwe, 1992, Wouters, 1992]. Incertain tissues, including testis, skin and lung and in numerous celllines, such as NIH3T3 fibroblasts, HL 60 myelomonocytic leukemic cells,F9 and P19 murine embryonal carcinoma cell lines and MCF7, RA metabolismcan be induced by RA pretreatment [Frolik, 1979, Roberts, 1979a and b;Duell, 1992; Wouters, 1992]. Studies involving targeted disruption ofRAR genes in F9 cells suggest that RAR-α and RAR-γ isoforms may play arole in regulating the enzymes responsible for this increased metabolism[Boylan, 1995].

The glucuronidation of RA is a significant metabolic step in theinactivation of RA [Blaner, 1994; Formelli, 1996]. The elimination of RAmay require oxidation to 4-oxo, followed by conjugation to form the4-oxo all-trans RA glucuronide. This is supported by studies in bothprimates and humans showing that the 4-oxo RA glucuronide is the onlyretinoid conjugate found in urine [Muindi, 1992; Muindi, 1994]. The factthat following RA therapy, 4-oxo RA is not present or barely detectablein serum, suggests that oxidation may be the rate limiting step in thisprocess.

It has recently been shown that 4-oxoretinol (4-oxo-ROL) can havegreater biological activity than retinol. The 4-oxo-ROL is inducible byRA in F9 and P19 mouse teratocarcinoma cells [Blumberg et al., 1995;Achkar et al., 1996].

It is known that zebrafish fins regenerate through an RA sensitiveprocess which utilizes many gene regulatory pathways involved in earlyvertebrate development [White, 1994; Akimenko, 1995a & b].

Cytochome P450s and Retinoic Acid Metabolism

In 1979, Roberts et al., [Roberts (1979a] first postulated that thecatabolism of retinoic acid (RA) was mediated by a cytochrome P450enzyme. Several P450s have since been shown to metabolize RA, includingP450 proteins from human, zebrafish and mouse. For example, humanP450RAI, which is induced by RA, metabolizes RA to more poplarderivatives including 4-hydroxy retinoic acid (4-OHRA) and 4-oxoretinoic acid (4-oxo RA) [White et al. (1996a)]. Since RA is useful asan antitumor agent, it is desirable to maintain high tissue levels ofRA. Thus, cytochrome P450 inhibitors that block RA metabolism, resultingin increased tissue levels of RA, may be useful therapeutic agents inthe treatment of cancers, such as prostate cancer [Wouters et al.,(1992); and De Coster et al., (1996)].

International Patent Publication No. WO 97/49815, published Dec. 31,1997, describes a family retinoid metabolizing proteins, CYP26A,including proteins from human, zebrafish and mouse and their codingsequences. This earlier publication is incorporated herein in itsentirety. cDNAs encoding a cytochrome P450-dependent enzyme (P450RAI)which is induced by RA have been cloned and characterized from zebrafishand the protein metabolizes RA to more polar derivatives including4-hydroxy retinoic acid (4-OH RA) and 4-oxo retinoic acid (4-oxo RA)[White et al., 1996a]. The identification of P450RAI gene is animportant step in the understanding of RA signaling but its presence hasbeen known since Roberts et al. (1979a) first postulated that thecatabolism of RA was mediated by a P450 enzyme [Frolik et al., 1979;Roberts et al., 1979a]. More recently, the isolation of cDNAs whichencode the full-length human and mouse P450RAI orthologs whoseexpression, like that of the fish cytochrome, is highly inducible by RAhas been achieved [Fujii et al., 1997; Ray et al., 1997]. Human andmouse genomic P450RAI-1 sequences are identified herein as SEQ ID NOS:15 and 16. The mouse sequence encoding P450RAI-1 is identified herein asSEQ ID NO: 17. Homologs have also been isolated from human, mouse, chickand xenopus all exhibiting a high degree of sequence conservation[Abu-Abed et al., 1998; Hollermann et al., 1998; White et al., 1997].There is extensive identity between the human and fish P450RAI geneswhich overall is 68% at the amino acid level (over 90% between mouse andhuman).

MCF7 cells have been shown to have RA inducible RA metabolism [Butlerand Fontana, 1992; Wouters et al., 1992]. The expression of P450RAI inthese cells is dependent on the continuous presence of RA [White et al.,1997]. This suggests that P450RAI regulation by RA forms anautoregulatory feedback loop that functions to limit localconcentrations of RA, such that when normal physiological levels of RAare exceeded, induction of P450RAI acts to normalize RA levels. Theinducible expression of P450RAI in mouse embryos also suggests that asimilar autoregulatory mechanism may limit exposure to RA sensitivetissues during development [Iulianella et al., 1999].

Retinoic Acid, Cytochrome p450 and Embryonic Development

All-trans-RA is a critical regulator of gene expression during embryonicdevelopment and in the maintenance of adult epithelial tissues [Gudas,et al. (1994); Lotan, R. M. (1995); Lotan, R. (1996); Morriss-Kay, G. M.(1996)]. The effects of all-trans-RA are mediated by heterodimers ofnuclear receptors for retinoic acid (RARs) and retinoid-X-receptors,which are regulated by by the 9-cis isomer of RA. Three differentsubtypes exist for each of these receptors (RARα, β and γ; RXR RAR α, βand γ) which individually are expressed in a tissue specific manner butcollectively can be found in essentially all cell types, both duringembryonic development and in the adult [Chambon, P. (1995).]. Theactivity of RA in these tissues is controlled, to a large extent, byenzymes involved in its synthesis from retinaldehyde (ALDH-1 andRALDH-2) and its catabolism to 4-OH, 4-oxo and 18-OH products (P450RAI)[White J. A., et al. (1997); Iulianella, A. et al. (1999); McCaffery P.et al., (1999) Niederreither, K. et al. (1999) Swindell E., et al.(1999)].

The present inventor and others have shown that P450RAI-1 (CYP26A) fromzebrafish, mouse, human, chick and xenopus which is responsible for themetabolism of active all-trans-RA to inactive polar metabolitesincluding 4-OH-RA, 4-oxo-RA and 18-OH-RA [White J., et al. (1997);Swindell E., et al. (1999); White, J. & Petkovich, M. (1996); Abu-Abed,et al. (1998); Fujii, H. et al. (1997); Ray, W. et al. (1997);Hollermann, T et al. (1998)]. P450RAI-1 expression can be induced byall-trans-RA pre-treatment in multiple tissues, and cell types, and thisexpression is concomitant with increased all-trans-RA catabolism. InMCF7 cells, all all-trans-RA suggesting a feedback-loop mechanism isdependent on the continued presence of all-trans-RA suggesting afeedback-loop mechanism for the regulation of all-trans-RA levels [WhiteJ., et al. (1997)]. Inducible expression of P450RAI-1 has also beenobserved in vivo in zebrafish, chick, xenopus and mouse embryossuggesting that this autoregulatory feedback-loop plays an importantrole in balancing all-trans-RA levels in certain developing tissues.

Studies from several groups show that tissues such as neural folds inchick embryos [Swindell E., et al. (1999)], caudal neuroepithelia[Iulianella, A et al. (1999); Fujii, H. et al. (1997)] and developingretina [McCaffery P. et al. (1999)] from mouse express P450RAI-1constitutively thus forming a barrier to all-trans-RA exposure.Comparison of the expression patterns of RALDH-2 and P450RAI-1 in thesemodels suggest that these enzymes act together to form regions of RAsynthesis and activity (where RALDH-2 is expressed). RALDH-2 expressingtissues have been shown to contain retinoid activity as measured by bothretinoid responsive reporter gene activity and direct measurement of RAlevels from tissue extracts; by similar analyses, P450RAI-1 expressingtissues do not [Iulianella, A et al. (1999); McCaffery P. et al.(1999)]. In addition, over expression of P450RAI-1 in xenopus embryoshas been shown to abrogate the teratogenic effects of exogenouslyapplied RA, consistent with a catabolic role for its enzyme [Hollermann,T et al. (1998)].

SUMMARY OF THE INVENTION

The present inventors have identified and characterized a novelcytochrome P450 that can metabolize retinoic acid, preferably all-transretinoic acid, (hereinafter referred to as P450RAI-2) and the nucleicacid sequence encoding therefor.

In one embodiment the P450RAI-2 is a mammalian P450RAI-2, and preferablya murine, rat or human P450RAI-2. In an another embodiment the P450RAI-2is a zebrafish P450RAI-2.

Although, the P450RAI-2 and encoding nucleic acid sequence of theinvention can be isolated and characterized from a number of differenttissues such as spleen, kidney, skeletal muscle, brain, liver, retina,heart or small intestine, it is preferably isolated and characterizedfrom brain cells, such as from from the cerebellum, cerebal cortex,medulla, occipital pole, frontal lobe and temporal lobe, and mostpreferably from the cerebellum.

Accordingly, the present invention provides an isolated nucleic acidmolecule comprising a sequence encoding a P450RAI-2, preferably a humanP450RAI-2 or a murine P450RAI-2 or fragments thereof.

In a preferred embodiment, an isolated nucleic acid molecule is providedhaving: (a) a nucleic acid sequence as shown in SEQ ID NOS: 4, 5, 28,27, 7, 18, 26, 21, 22, 23, 24, or 25 where T can also be U; (b) nucleicacid sequences complementary to (a); (c) nucleic acid sequences whichare homologous to (a) and (b); (d) a nucleic acid molecule differingfrom any of the nucleic acid molecules of (a) to (c) in codon sequencesdue to the degeneracy of the genetic code; or (e) a fragment of (a) to(d) that is at least 15 bases, preferably 20 to 30 bases, and which willhybridize to (a) to (c) under stringent hybridization conditions.

The present invention also includes the P450RAI-2 polypeptide itself.Accordingly, the invention provides a polypeptide having an amino acidsequence of a P450RAI-2. Preferably, the invention provides apolypeptide having either the human (SEQ ID NO: 5) or a homologous mousesequence or fragment thereof. The invention also comprises peptidescomprising fragments of the amino acid sequence of SEQ ID NO: 5.Preferably the fragments comprise amino acid sequences of SEQ ID NOS: 11or 12 or encoded by nucleic acid sequences SEQ ID NOS. 18, 26, or 21 to25. In another embodiment the fragments preferably comprise at least 14amino acid residues and are most preferably antigenic or immunogenic. Inone embodiment the invention provides peptides encoded by a nucleic acidsequence of SEQ ID NO: 4 or fragments thereof and to an antisensenucleic acid molecule to all or part of the nucleic acid moleculeencoding P450RAI-2.

In another embodiment, homologs, analogs, and modified proteins of theinvention as described herein are encompassed within the scope of thisinvention.

In one embodiment, the invention also provides a nucleic acid moleculeof the invention operationally linked to an expression control sequencein a suitable expression vector. In another embodiment, the expressionvector comprising the nucleic acid molecule of the invention is capableof being activated to express the peptide which is encoded by thenucleic acid molecule and is capable of being transformed or transfectedinto a suitable host cell. Such transformed or transfected cells arealso encompassed with the scope of this invention.

The invention also provides a method of preparing a P450RAI-2 protein ofthe invention utilizing a nucleic acid molecule of the invention. In oneembodiment, a method for preparing a P450RAI-2 protein of the inventionis provided comprising: transforming a host cell with a recombinantexpression vector comprising a nucleic acid sequence of the invention;(b) selecting transformed host cells from untransformed host cells; (c)culturing a selected transformed host cell under conditions which allowexpression of the protein; and (d) isolating the protein.

The invention also encompasses an antibody specific for one or moreepitopes of a protein of the invention, such as a peptide specificantibody or a polyclonal antibody, and more preferably a monoclonalantibody. The invention also encompasses methods for preparing theantibodies. Preferably the epitopes are selected from the groupconsisting of SEQ ID NOS: 5, 11, 12, or those encoded by nucelic acidsequences SEQ ID NOS; 4, 6, 8, 18, 21-25, 27 or 28 or immunogenicfragments thereof.

The invention also includes a method for detecting a disease or medicalcondition associated with P450RAI-2 expression or RA metabolism in ananimal. “A disease or medical condition associated with P450RAI-2expression” as used herein means any disease that can be affected orcharacterized by the level of P450RAI-2 expression. This includes,without limitation, diseases affected by, high, normal, reduced ornon-existent expression of P450RAI-2 or expression of mutated P450RAI-2.A disease or medical condition associated with P450RAI-2 expressionincludes diseases associated with RA metabolism such as cell cycleregulation, particularly cell growth and apoptosis, for instance cancer,dysplasia, autoimmune disease, dermatological disorders and disabilitiesassociated with high order brain functions, such as learning and memory.The method comprises assaying for the P450RAI-2 from a sample, such as ablood sample, a biopsy, or other cellular or tissue sample, from ananimal susceptible of having such a disease. In one embodiment, themethod comprises contacting the sample with an antibody of the inventionthat binds P450RAI-2, and measuring the amount of antibody bound toP450RAI-2 in the sample, or unreacted antibody. In another embodiment,the method involves detecting the presence of a nucleic acid moleculehaving a sequence encoding a P450RAI-2, comprising contacting the samplewith a nucleotide probe which hybridizes with the nucleic acid molecule,preferably mRNA or cDNA to form a hybridization product under conditionswhich permit the formation of the hybridization product, and assayingfor the hybridization product.

The invention further includes a kit for detecting a disease orcondition associated with P450RAI-2 expression in a sample comprising anantibody of the invention, preferably a monoclonal antibody. Preferablydirections for its use is also provided. The kit may also containreagents that are required for binding of the antibody to a P450RAI-2protein in the sample.

The invention also provides a kit for detecting the presence of anucleic acid molecule having a sequence encoding a polypeptide relatedto or analogous to a polypeptide of the invention, comprising anucleotide probe which hybridizes with the nucleic acid molecule,reagents required for hybridization of the nucleotide probe with thenucleic acid molecule, and directions for its use.

The invention further provides a method of treating or preventing amedical condition disease associated with P450RAI-2 or RA expressioncomprising administering an effective amount of an agent that activates,simulates or inhibits P450RAI-2 expression, as the situation requires,to an animal in need thereof. In a preferred embodiment, P450RAI-2, atherapeutically active fragment thereof, or an agent which activates orsimulates P450RAI-2 expression is administered to the animal in needthereof to treat cancer, dysplasia, autoimmune disease or dermatologicaldisorders or to improve high order brain functions or dermatologicaldisorders. In another embodiment the disease is associated with overexpression of P450RAI-2 or too little apoptosis, and the method oftreatment comprises administration of an effective amount of an agentthat inhibits P450RAI-2 expression such as an antibody to P450RAI-2, amutation thereof, or an antisense nucleic acid molecule to all or partof the P450RAI-2 gene.

In another embodiment, the invention provides pharmaceuticalcompositions comprising the nucleic acid molecules of proteins,antibodies, vectors or cells of the invention and a pharmaceuticallyacceptable carrier.

In another embodiment, the invention further provides a method foridentifying modulators of P450RAI-2 expression or P450RAI-2 activity.

In yet another embodiment, the invention further provides a method ofrational drug design.

In one embodiment the invention provides methods or uses of the proteinsand nucleic acid molecules of the invention, such as in relation tomedical treatment.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only. Various changes and modificationswithin the spirit and scope of the invention will become apparent tothose skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic diagram showing the 6 exons of human cytochromep450RAI-2 on human clone having GenBank Accession No. AC007002 (SEQ IDNO:3). The numbers above the schematic diagram indicate the amino acidregions of the exons and the numbers below the schematic refer tonucleotide positions on the human sequence.

FIG. 2 Human P450RAI-2 cDNA sequence (SEQ ID NO: 28) comprising thecoding sequence and the 3′ untranslated sequence. The full-length cDNAclone was isolated from human retina cDNA. The deduced primary sequenceusing single-letter amino acid codes, identifies a 512 amino acidprotein which is shown directly below the corresponding nucleotidesequence. Numbers on the right refer to the nucleotide positions.

FIG. 3 Sequence comparison between human P450RAI-2 (SEQ ID No:5) andhuman P450RAI-1 (SEQ ID No:13). Predicted amino acid sequences werealigned using Omiga software (Oxford Molecular, CA). Identical aminoacids are highlighted by the black boxes with white letters.Conservatively substituted amino acids are indicated by the open boxes.Gaps, indicated by the dashes, have been introduced in several regionsin order to optimize amino acid identity between the two proteins.Overall the two protein sequences show 42% identity at the amino acidlevel. Numbers on the right hand side refer to the corresponding aminoacid positions.

FIG. 4 Expression of P450RAI-2 in human tissues. RNA samples from 76normal human tissues were probed for expression of P450RAI-2 transcriptsusing a commercially available dot blot (A). Signals representingP450RAI-2 transcripts are observed in three samples, a2, b2 and h1representing left and right cerebellum and pons respectively. Sample a1is whole brain and a11 is fetal brain for comparison. Controlhybridization with a human ubiquitin probe (B) shows differences in RNAloading. Northern blot analyses for expression of P450RAI-2 expressionin human brain (D). 2 μg poly A+ mRNA each from eight different humanbrain tissues was used to analyze P450RAI-2 expression. Transcripts atapproximately 5 Kb corresponding to P450RAI-2 are indicated, with thehighest levels of expression seen in cerebellum.

FIG. 4C shows the location of the different human mRNAs on the blot usedin FIG. 4A.

FIG. 5 shows northern blot analysis of human cell lines probed with anα-[³²P]-dATP labeled probe having the sequence identified as SEQ ID NO:4SKMES; CALU-1 and MCF-7 (A). Cells were treated with DMSO, all-transretinoic acid, 9-cis retinoic acid or 13-cis retinoic acid. Cells wereexposed to 10⁻⁶ M final concentrations of each retinoid dissolved inDMSO. Transcripts corresponding to P450RAI-2 are indicated by thearrowhead. The blot was also probed with the human β-actin probe tocontrol for RNA loading of the gel, shown in the middle panel (B). The18S and 28S portions of the mRNA as seen on the ethidium bromide stainedagarose gel are shown in the bottom panel (C).

FIG. 6 is similar to FIG. 5 except that the cells, HPK1A-RAS, weretreated with either DMSO or all-trans retinoic acid.

FIG. 7 All-trans-RA induction of P450RAI-2 expression. Northern blotanalysis (A) of cultured cells treated with all-trans-RA or vehicle(DMSO). P450RAI-2 hybridizing transcripts are identified. The positionsof 28S and 18S ribosomal RNA are indicated along with the ethidiumbromide stained gel showing the relative abundance of RNA in allsamples. Multiple other cell lines were tested using semiquantitativeRT-PCR and southern blotting (B). Transcripts for P450RAI-2 areregulated in a cell specific manner. P450RAI-2 is constitutivelyexpressed in SK-MES-1 and SW900 and possibly WTE; inducible in MCF-7,HPK1a-ras and HeLa; and undetectable in SK-Luci-6, V79 or NB4. Atimeline of induction of mRNAs, for P450RAI-2 in HPK1a-ras cells (C).Within 2 hours of addition of all-trans-RA maximal induction oftranscripts for P450RAI-2 is observed. GAPDH controls are shown belowfor each RNA sample analyzed.

FIG. 8A shows the total aqueous soluble radioactivity measured usingaliquots of the aqueous soluble extracts from media alone, as well ascells transfected with pcDNA3.1, pcDNA3.1-CYP26A (human) (i.e., P450RAI)or pcDNA-P450RAI-2. Aqueous soluble extracts were subjected toβ-scintillation counting.

FIG. 8B shows a summary of the peak integration analysis performed afterHPLC on the organic soluble radioactivity. Samples were the same as inFIG. 8A. Cells transfected with either pcDNA3.1-CYP26A (human) orpcDNA3.1-P450RAI-2 show a decrease in all-trans retinoic acid substratewith a concomitant increase in the production of 4-OH-retinoic acid,4-oxo-retinoic acid and more polar peaks.

FIG. 9 shows the same analysis as FIG. 8B except that cells were treatedwith 1 μM non-radioactive all-trans-retinoic acid.

FIG. 10 shows a control HPLC trace from media alone in the absence ofthe COS-1 cells. An all-trans-retinoic acid substrate peak is observedat 20.808 minutes. Peaks at 1.409 and 1.874 are contaminants notcharacteristic of retinoids. The top panel shows photo diode arraydetection of the peaks. Retinoids have characteristic UV maxima in therange of about 320 to about 380 nM.

FIG. 11 is similar to FIG. 10 except that the sample is from COS-1 cellstransfected with the pcDNA3.1 plasmid alone.

FIG. 12 is similar to FIG. 10 except that the sample is from COS-1 cellstransfected with pcDNA3.1-P450RAI. Multiple more polar peakscharacteristic of retinoids are generated in these cells. Peaks whichco-elute with standards for 4-OH-retinoic acid and 4-oxo-retinoic acidwere observed at 8.191 and 9.661 minutes respectively. Additional peakswhich have not been characterized are also evident.

FIG. 13 is similar to FIG. 12 except that the sample is from COS-1 cellstransfected with pcDNA3.1-P450RAI-2.

FIG. 14 shows HPLC analysis of all-trans-RA metabolism. COS-1 cells weretransiently transfected with pcDNA3.1-P450RAI-2 (A), pcDNA3.1-P450RAI-1(B) or pcDNA3.1 alone (C) and exposed to μM all-trans-RA for 3 hours.Incubation with RA was followed by total lipid extraction of the mediaand subsequent HPLC analysis using a reverse-phase system. Expression ofeither P450RAI-2 or P450RAI-1 in cells causes disappearance ofall-trans-RA substrate (compare C to A or B) in addition to thegeneration of more polar metabolic products. Identities of the retinoidslabeled as all-trans-RA, 4-OH-RA, 4-oxo-RA and 18-OH-RA (A and B) wereverified by co-elution with known standards and comparison of thespectral properties of the peaks using photodiode array detection.Multiple polar peaks are observed in P450RAI-2 expressing cells exposedto all-trans-RA. Peaks labeled 1-4 (A) have spectral propertiescharacteristic of retinoids, specifically a UV maxima of between 320 and350 nm. The exact identity of these polar metabolites remains to beestablished.

FIG. 15 shows metabolism of all-trans-RA. COS-1 cells transientlytransfected with pcDNA3.1-P450RAI-2, pcDNA3.1-P450RAI-1 or pcDNA3.1alone and exposed to 100 nM [³H]all-trans-RA for 3 hours. Conversion ofall-trans-RA to aqueous-soluble metabolites is observed in P450RAI-2 orP450RAI-1 expressing cells compared to pcDNA vector or media alonecontrol samples (A). Using HPLC analysis with subsequent β-scintillationcounting was used to evaluate the lipid-soluble retinoids generated fromP450RAI-2 or P450RAI-1 expressing cells. Fractions from chromatographywere grouped into three regions, all-trans-RA substrate, 4-OH region andpolar region allowed quantification of the retinoid metabolites. Levelsof all-trans-RA remaining after incubation were substantially decreasedin P450RAI-2 or P450RAI-1 transfected cells compared to controls (B).Additionally, there is an increase in radioactivity representing boththe 4-OH and polar regions (B).

FIG. 16 A-D is competitive inhibition of P450RAI-mediated all-trans-RAmetabolism. COS 1 cells transiently transfected with pcDNA3.1-P450RAI-2,pcDNA3.1-P450RAI-1 or pcDNA3.1 alone were used to assess the ability ofseveral retinoids to competitively inhibit all-trans-RA metabolism.Cells were exposed to 2 nM [³H]all-trans-RA with increasingconcentrations of unlabelled competitor and assayed for generation ofaqueous soluble radioactivity. Panels on the right show cells expressingP450RAI-2 with panels on the left showing cells expressing P450RAI-1.9-cis-RA and 13-cis-RA (top panels) are less effective than all-trans-RAas competitors for either P450RAI-2 or P450RAI-1. Retinol and retinalwere similarly tested (bottom panels) and found to be less effectivecompetitors. For comparison, the nonspecific cytochrome P450 inhibitorketoconazole is shown in each panel.

FIG. 17 shows Northern blot (A) and RT-PCR (B) results for total RNAsamples from the various cell samples designated.

FIG. 18 shows expression of P450RAI-2 in 8.0 and 8.5 dpc mouse embryos.(A) 8.0 dpc lateral view. No apparent staining. (B) 8.0 dpc, dorsalview. Staining at anterior end of neutral folds. (C) 8.5 dpc, lateralview. Expression is evident, possibly in presumptive rhombmeres 2, 5,and 6. (D) 8.5 dpc, dorsal view, rhombomere expression of RAI2 isclearly evident. TL: Tail; YS Yolk Sac; NF: Folds; pr: PresumptiveRhombomeres.

FIG. 19 shows expression of P450RAI2 in 9.0 and 10.5 dpc mouse embyros.(A) 9.0 dpc, lateral view. Specific staining is visible in the eye, andrhombomeres 5 and 6. Diffuse staining is visible where the hind bud isbeginning to form. (B) 9.0 dpc, dorsal view. Rhombomeres 5 and 6 showRAI2 expression. (C) 10.5 dpc, lateral view. The otic vesicle and eyeare stained. (D) 10.5 dpc, dorsal view. Specific staining is observed inboth otic vesicles as well as as the hind linb bud. HL: hind limb bud;OV: Otic Vesicle.

FIG. 20 shows expression of P450RAI2 staining in 11.5 dpc mouseembryo(A) 11.5 dpc, laterial view, staining is visible in both the foreand hindlimb bud. (B) 11.5 dpc, ventral view. Expression of RAI2 in bothlimb buds (C) Close up of forelimb bud, showing a lack of expression inthe apical ectodermal ridge FL: Forelimb bud; HL: Hindlimb bud; AR:Apical Ectodermal Ridge.

FIG. 21 shows P450RAI2 staining in embryos treated with Retinoic Acid(A) 8.5 dpc, lateral view, staining is observed in rhombomere 5 and thetail mesoderm as indicated by the arrow. (B) 8.5 dpc, dorsal viewclearly showing P450RAI2 expression in rhombomere 5. (C) 9.5 dpc,lateral view, expression of P450RAI2 is observed in rhombomeres 5 and 6,the developing hindlinb, somites and posterior mesoderm. (D) 9.5 dpc,dorsal view, expression is evident in rhombomeres 3,5 and 6 and in trunkectoderm as indicated by the arrow. r: rhombomere; HL; Limb bud.

FIG. 22 shows P450RAI2 expression in 11.5 dpc embryos treated withretinoic acid. (A) 11.5 dpc, lateral view, P450RAI2 expression isobserved in both the developing hind and fore limb. (B) 11.5 dpc,ventral view, as in embryos untreated with retinoic acid, P450RAI2expression is not observed in the aptical ectodermal ridge.

DETAILED DESCRIPTION OF THE INVENTION

Retinoids, particularly all-trans retinoic acid (all-trans-RA), arepotent regulators of cell differentiation, cell proliferation andapoptosis. As noted above, the role of all-trans-RA during developmentand in the maintenance of adult tissues has been well established. Thecontrol of all-trans-RA in cells and tissues is regulated by the balancebetween its biosynthesis and its catabolism to inactive metabolites. Thecytochrome P450 enzyme P450RAI-1 is partially responsible for thisinactivation of all-trans-RA.

The present inventors have now identified, cloned and characterized asecond related enzyme, here termed P450RAI-2, which is also involved inthe specific inactivation of all-trans-RA. A cDNA has been isolated fromhuman retina and sequenced. A protein encoded by the cDNA has beenexpressed and shown to have the ability to metabolize all-trans-RA tomore polar metabolites. The metabolites so formed include products thathave been oxidized at the 4-position of the β-ionone ring, including thecorresponding acid hydroxylated at the 4-position of the β-ionone ring.The mRNA has been found to be inducible in multiple cell types includingbut not limited to human lung and human skin upon the addition ofall-trans retinoic acid.

The present inventors herein show that tansiently transfected P450RAI-2can convert all-trans-RA to more polar metabolites including 4-oxo,4-OH, and 18-OH-retinoic acid. Competition experiments with otherretinoids suggest that all-trans-RA is the preferred substrate, but notnecessarily the only retinoid substrate. The high level of expression ofP450RAI-2 particularly in the cerebellum and pons of human adult brain,suggests a unique role for this enzyme in the protection of specifictissues from exposure to retinoids.

Homologs of the cloned sequence have also been identified. Partialnucleotide sequences have been determined for the mouse, rat andzebrafish P450RAI-2 coding sequence.

Definitions

The term “retinoids” as used herein means a group of compounds whichincludes retinoic acid, vitamin A (retinol) and a series of natural andsynthetic derivatives that can exert profound effects on development anddifferentiation in a wide variety of systems. For purposes of thisdisclosure “retinoid” is also intended to encompass an equivalentthereof having the same functional characteristics which may beproduced, for example, by computational chemistry.

The following standard abbreviations for the amino acid residues areused throughout the specification: A, Ala—alanine; C, Cys—cysteine; D,Asp—aspartic acid; E, Glu—glutamic acid; F, Phe—phenylalanine; G,Gly—glycine; H, His—histidine; I, Ile—isoleucine; K, Lys—lysine; L,Leu—leucine; M, Met—methionine; N, Asn—asparagine; P, Pro—proline; Q,Gln—glutamine; R, Arg—arginine; S, Ser—serine; T, Thr—threonine; V,Val—valine; W, Trp—tryptophan; Y, Tyr—tyrosine; and p.Y.,P.Tyr—phosphotyrosine.

I. Nucleic Acid Molecules of the Invention

The present invention provides an isolated nucleic aid moleculecomprising a sequence encoding a cytochrome P450RAI-2 polypeptide.

The term “isolated” refers to a nucleic acid substantially free ofcellular material or culture medium when produced by recombinant DNAtechniques, or chemical precursors, or other chemicals when chemicallysynthesized.

The term “nucleic acid molecule” is intended to include unmodified DNAor RNA or modified DNA or RNA. For example, the nucleic acid moleculesor polynucleotides of the invention can be composed of single- anddouble stranded DNA, DNA that is a mixture of single- anddouble-stranded regions, single- and double stranded RNA, and RNA thatis a mixture of single- and double-stranded regions, hybrid moleculescomprising DNA and RNA that may be single-stranded or, more typicallydouble stranded or a mixture of single- and double stranded regions. Inaddition, the P450RAI-2 nucleic acid molecules can be composed oftriple-stranded regions comprising RNA or DNA or both RNA and DNA. Thenucleic acid molecules of the invention may also contain one or moremodified bases or DNA or RNA backbones modified for stability or forother reasons. “Modified” bases include, for example, tritiated basesand unusual bases such as inosine. A variety of modifications can bemade to DNA and RNA; thus “nucleic acid molecule” embraces chemically,enzymatically, or metabolically modified forms. The term“polynucleotide” shall have a corresponding meaning.

One aspect of the present invention is thus an isolated nucleic acidmolecule comprising a nucleotide sequence selected from the groupconsisting of:

(a) a nucleotide sequence as shown in SEQ ID NOS: 4 or 28, butpreferably SEQ ID NO: 4, wherein T can also be U;

(b) nucleotide sequences complementary to (a);

(c) nucleotide sequences which are homologous to (a) or (b);

(d) a nucleotide sequence differing from any of the nucleotide sequencesof (a) to (c) in codon sequences due to the degeneracy of the geneticcode; or

(e) a fragment of (a) to (d) that is at least 15 bases, preferably 20 to30 bases, and which would hybridize to (a) to (d) under stringenthybridization conditions. In another embodiment, the fragment is atleast 35, 40, 45, 50, 55, or 60 or more nucelotides in length. Inanother embodiment the fragment is capable of oxidizing a retinoid. Inyet another embodiment it preferably has at least about 55 percenthomology with the protein encoded by a nucleotide sequence of (a) or(b).

In another embodiment, the nucleotide sequence in (a) above is a humanP450RAI-2 sequence. In one embodiment, the nucleic acid sequence can beused as a probe or a primer, such as for PCR, like SEQ ID NOS: 9, 10,29, 30, 33, 37 or 38. In yet another embodiment, the nucleotide sequenceof (a) above is selected from the group consisting of: a mouse P450RAI-2sequence, such as SEQ ID NO: 6, 18, 26, 21, 22, 23, 24 or 25; a ratP450RAI-2 sequence, SEQ ID NO: 27; or a zebrafish P450RAI-2 sequence,SEQ ID NO: 8.

In one embodiment, the nucleic acid molecule of the invention encodes aprotein that is capable of oxidizing a retinoid, preferably retinoicacid, preferably at the 4-position of the β-ionone ring. In anotherembodiment the nucleic acid molecule of the invention encodes a proteinhaving SEQ ID NO: 5. In another embodiment, the nucleotide sequenceinhibits P450RAI-2 expression, such as certain complimentary sequencesto SEQ ID NO 4.

In one embodiment of the invention, the nucleic acid molecule consistsof any of the nucleotide sequences described herein.

In all of the sequences referred to above, T can also be U. Aspreviously stated, the invention includes isolated DNA molecules havingsuch sequences of nucleotides, and RNA molecules having such sequences.The invention thus includes isolated mRNA transcribed from DNA havingsuch a sequence. The invention further encompasses nucleic acidmolecules that differ from any of the nucleic acid molecules of theinvention in codon sequences due to the degeneracy of the genetic code.

The invention also encompasses nucleic acid sequences or molecules thatare analogs of the nucleic acid sequences and molecules describedherein. The term “a nucleic acid sequence which is an analog” means anucleic acid sequence which has been modified as compared to thesequences described herein, such as sequences of (a), (b), (c), (d), or(e), above wherein the modification does not alter the utility of thesequences described herein. The modified sequence or analog may haveimproved properties over the sequence shown in (a), (b), (c), (d) or(e). One example of a modification to prepare an analog is to replaceone of the naturally occurring bases (i.e. adenine, guanine, cytosine orthymidine) of the sequence shown in SEQ ID NO: 4, 6, 8-10, 18, or 21-28with a modified base such as such as xanthine, hypoxanthine,2-aminoadenine, 6-methyl, 2-propyl and other alkyl adenines, 5-halouracil, 5-halo cytosine, 6-aza uracil, 6-aza cytosine and 6-aza thymine,pseudo uracil, 4-thiouracil, 8-halo adenine, 8-aminoadenine, 8-thioladenine, 8-thiolalkyl adenines, 8-hydroxyl adenine and other8-substituted adenines, 8-halo guanines, 8 amino guanine, 8-thiolguanine, 8-thiolalkyl guanines, 8-hydroxyl guanine and other8-substituted guanines, other aza and deaza uracils, thymidines,cytosines, adenines, or guanines, 5-trifluoromethyl uracil and5-trifluoro cytosine.

Another example of a modification is to include modified phosphorous oroxygen heteroatoms in the phosphate backbone, short chain alkyl orcycloalkyl intersugar linkages or short chain heteroatomic orheterocyclic intersugar linkages in the nucleic acid molecule shown inSEQ ID NOS: 4, 6, 8-10, 18, or 21-28. For example, the nucleic acidsequences may contain phosphorothioates, phosphotriesters, methylphosphonates, and phosphorodithioates.

A further example of an analog of a nucleic acid molecule of theinvention is a peptide nucleic acid (PNA) wherein the deoxyribose (orribose) phosphate backbone in the DNA (or RNA), is replaced with apolyamide backbone which is similar to that found in peptides (P. E.Nielsen, et al Science 1991, 254, 1497). PNA analogs have been shown tobe resistant to degradation by enzymes and to have extended lives invivo and in vitro. PNAs also bind stronger to a complimentary DNAsequence due to the lack of charge repulsion between the PNA strand andthe DNA strand. Other nucleic acid analogs may contain nucleotidescontaining polymer backbones, cyclic backbones, or acyclic backbones.For example, the nucleotides may have morpholino backbone structures(U.S. Pat. No. 5,034,506). The analogs may also contain groups such asreporter groups, a group for improving the pharmacokinetic orpharmacodynamic properties of nucleic acid sequence.

It will be appreciated that the invention includes nucleic acidmolecules encoding truncations of proteins of the invention, and analogsand homologs of proteins of the invention and truncations thereof, asdescribed below. It will further be appreciated that variant forms ofnucleic acid molecules of the invention which arise by alternativesplicing of an mRNA corresponding to a cDNA of the invention areencompassed by the invention. The invention further includesbiologically active fragments of the nucleic acid molecules of theinvention. Such fragments would include, but is not necessarily limitedto any nucleic acid molecules which are beneficial in the modulation,including but not limited to simulation, inhibition or stimulation ofP450RAI-2 activity or P450RAI-2 expression, or in the identification orproduction of such agents.

A nucleic acid molecule of the invention can encode a protein(polypeptide) having a homology of at least about 50, at least about 55,or more preferably at least about 58 percent with a protein encoded bySEQ ID NO:4 or the full length anti-sense sequence thereto. The level ofhomology, according to various aspects of the invention is at leastabout 60 percent; at least about 63 percent; at least about 65 percent;at least about 68 percent; at least about 70 percent; at least about 73percent; at least about 75 percent; at least about 78 percent; at leastabout 80 percent; at least about 83 percent; at least about 85 percent;at least about 88 percent; at least about 90 percent; at least about 93percent; at least about 95 percent; or at least about 98 percent.Methods for aligning the sequences to be compared and determining thelevel of homology between the sequences are described in detail below.

In another aspect, the present invention includes a fragment of thenucleotide sequence encoding P450RAI-2 (SEQ ID NO:4). Such a fragmentcan find usefulness as a probe or depending on the fragment may evenhave biological activity itself. The complement of the probe can findutility in, for example, manufacture of the probe or inhibition of anyactivity of the fragment, as the case may be. In a particular use, theprobe can be used to determine the presence of an RNA molecule in asample which might, or might not, also include an RNA molecule encodingP450RAI-1. Such a probe would generally be 20 nucleotides long or be atleast 20 nucleotides long. The probe could also be 25, 30, 35, 40, 45,50, 55, 60 or more nucleotides in length and the probe can include thefull length of the complement to the sequence to which it is intended tobind. The sequence of the probe would also be sufficientlydistinguishable from any portion of the sequence encoding P450RAI-1 thatit would not cross-hybridize to a significant extent to a nucleotidesequence that encodes P450RAI-1, or portion thereof, particularly to anRNA encoding P450RAI-1. Such a probe would thus be sufficientlydifferent from any sequence of contiguous nucleotides selected from thenucleotide sequence encoding human P450RAI-1 (SEQ ID NO:13) that thereis no more than about 60% homology between the two sequences when thetwo sequences are directly aligned with each other. More preferably, thepercent homology would be less than about 55%, or less than about 50%,or less than about 45%, or even less than about 40%. Certain probes ofthe invention are selected so as span borders between introns of thecoding sequence as determined from the genomic sequence (SEQ ID NO:3).

The invention includes the method of determining the presence of anucleic acid molecule encoding P450RAI-2 in a sample containing RNAisolated from a human cell, using such a probe.

In the context of this specification, the term “conserved” describessimilarity between sequences. The degree of conservation between twosequences can be determined by optimally aligning the sequences forcomparison. Here, sequences were aligned using the Omiga softwareprogram, Version 1.13. (Oxford Molecular Group, Inc., Campbell, Calif.).The Omiga software uses the Clustal W Alignment algorithms [Higgins etal., 1989; Higgins et al., 1991; Thompson et al. 1994] Default settingsused are as follows: Open gap penalty 10.00; Extend gap penalty 0.05;Delay divergent sequence 40 and Scoring matrix—Gonnet Series. Percentidentity or homology between two sequences is determined by comparing aposition in the first sequence with a corresponding position in thesecond sequence. When the compared positions are occupied by the samenucleotide or amino acid, as the case may be, the two sequences areconserved at that position. The degree of conservation between twosequences is often expressed, as it is here, as a percentagerepresenting the ratio of the number of matching positions in the twosequences to the total number of positions compared.

In one particular aspect, the present invention is a nucleic acidmolecule of any preceding claim which encodes a protein that is aconservatively substituted variant of the protein encoded by thenucleotide sequence of SEQ ID NO:4.

Further, it will be appreciated that the invention includes nucleic acidmolecules comprising nucleic acid sequences having substantial sequencehomology with the nucleic acid sequences as shown in SEQ ID NO. 4, 6,8-10, 18, or 21-28 and fragments thereof. The term “sequences havingsubstantial sequence homology” means those nucleic acid sequences thathave slight or inconsequential sequence variations from these sequences,i.e., the sequences function in substantially the same manner to producefunctionally equivalent proteins. The variations may be attributable tolocal mutations or structural modifications.

Nucleic acid sequences having substantial homology include nucleic acidsequences having at least 85%, preferably 90-95% identity with thenucleic acid sequence as shown in SEQ ID NO: 4, 6, 8-10, 18, or 21-28.However, the invention is not to be restricted by this homology, forinstance, nucleic acid sequences having at least a 50% homology with thesequence shown in 4, 6, 8-10, 18, or 21-28 are also encompassed withinthe scope of the present invention.

“Stringent hybridization conditions” is a term known to a person skilledin the art. Appropriate stringency conditions which promote nucleic acidhybridization, for example, 6× sodium chloride/sodium citrate (SSC) atabout 45° C. are know. The following examples are found in CurrentProtocols in Molecular Biology, John Wiley & Sons, NY (1989),6.3.1-6.3.6: For 50 ml of a first suitable hybridization solution, mixtogether 24 ml formamide, 12 ml 20×SSC, 0.5 ml 2 M Tris-HCl pH 7.6, 0.5ml 100× Denhardt's solution, 2.5 ml deionized H₂O, 10 ml 50% dextransulfate, and 0.5 ml 10% SDS. A second suitable hybridization solutioncan be 1% crystalline BSA (fraction V), 1 mM EDTA, 0.5 M Na₂HPO₄ pH 7.2,7% SDS. The salt concentration in the wash step can be selected from alow stringency of about 2×SSC at 50° C. to a high stringency of about0.2×SSC at 50° C. Both of these wash solutions may contain 0.1% SDS. Inaddition, the temperature in the wash step can be increased from lowstringency conditions at room temperature, about 22° C., to highstringency conditions, at about 65° C. The cited reference gives moredetail, but appropriate wash stringency depends on degree of homologyand length of probe. If homology is 100%, a high temperature (65° C. to75° C.) may be used. If homology is low, lower wash temperatures must beused. However, if the probe is very short (<100 bp), lower temperaturesmust be used even with 100% homology. In general, one starts washing atlow temperatures (37° C. to 40° C.), and raises the temperature by 3-5°C. intervals until background is low enough not to be a major factor inautoradiography.

Isolated nucleic acid molecules having sequences which differ from thenucleic acid sequence shown in SEQ ID NO: 4, 6, 8-10, 18, or 21-28 dueto degeneracy in the genetic code are also within the scope of theinvention. Such nucleic acids encode functionally equivalent proteinsbut differ in sequence from the above mentioned sequences due todegeneracy in the genetic code.

An isolated nucleic acid molecule of the invention which comprises DNAcan be isolated by preparing a labelled nucleic acid probe based on allor part of the nucleic acid sequences as shown in SEQ ID NO: 4, 6, 8-10,18, or 21-28 and using this labelled nucleic acid probe to screen anappropriate DNA library (e.g. a cDNA or genomic DNA library). Forexample, a genomic library isolated can be used to isolate a DNAencoding a novel protein of the invention by screening the library withthe labelled probe using standard techniques. Nucleic acids isolated byscreening of a cDNA or genomic DNA library can be sequenced by standardtechniques.

An isolated nucleic acid molecule of the invention which is DNA can alsobe isolated by selectively amplifying a nucleic acid encoding a novelprotein of the invention using the polymerase chain reaction (PCR)methods and cDNA or genomic DNA. It is possible to design syntheticoligonucleotide primers from the nucleic acid sequence as shown in SEQID NO: 4, 6, 8-10, 18, or 21-28 for use in PCR. A nucleic acid can beamplified from cDNA or genomic DNA using these oligonucleotide primersand standard PCR amplification techniques. The nucleic acid so amplifiedcan be cloned into an appropriate vector and characterized by DNAsequence analysis. It will be appreciated that cDNA may be prepared frommRNA, by isolating total cellular mRNA by a variety of techniques, forexample, by using the guanidinium-thiocyanate extraction procedure ofChirgwin et al., Biochemistry, 18, 5294 5299 (1979). cDNA is thensynthesized from the mRNA using reverse transcriptase (for example,Moloney MLV reverse transcriptase available from Gibco/BRL, Bethesda,Md., or AMV reverse transcriptase available from Seikagaku America,Inc., St. Petersburg, Fla.).

An isolated nucleic acid molecule of the invention which is RNA can beisolated by cloning a cDNA encoding a novel protein of the inventioninto an appropriate vector which allows for transcription of the cDNA toproduce an RNA molecule which encodes a protein of the invention. Forexample, a cDNA can be cloned downstream of a bacteriophage promoter,(e.g., a T7 promoter) in a vector, cDNA can be transcribed in vitro withT7 polymerase, and the resultant RNA can be isolated by standardtechniques.

A nucleic acid molecule of the invention may also be chemicallysynthesized using standard techniques. Various methods of chemicallysynthesizing polydeoxynucleotides are known, including solid-phasesynthesis which, like peptide synthesis, has been fully automated incommercially available DNA synthesizers (See e.g., Itakura et al. U.S.Pat. No. 4,598,049; Caruthers et al. U.S. Pat. No. 4,458,066; andItakura U.S. Pat. Nos. 4,401,796 and 4,373,071).

Determination of whether a particular nucleic acid molecule encodes anovel protein of the invention may be accomplished by expressing thecDNA in an appropriate host cell by standard techniques, and testing theactivity of the protein using the methods as described herein. A cDNAhaving the activity of a novel protein of the invention so isolated canbe sequenced by standard techniques, such as dideoxynucleotide chaintermination or Maxam-Gilbert chemical sequencing or by automated DNAsequencing, to determine the nucleic acid sequence and the predictedamino acid sequence of the encoded protein.

The initiation codon and untranslated sequences of nucleic acidmolecules of the invention may be determined using currently availablecomputer software designed for the purpose, such as PC/Gene(IntelliGenetics Inc., California). Regulatory elements can beidentified using conventional techniques. The function of the elementscan be confirmed by using these elements to express a reporter genewhich is operatively linked to the elements. These constructs may beintroduced into cultured cells using standard procedures. In addition toidentifying regulatory elements in DNA, such constructs may also be usedto identify proteins interacting with the elements, using techniquesknown in the art.

The sequence of a nucleic acid molecule of the invention may be invertedrelative to its normal presentation for transcription to produce anantisense nucleic acid molecule. The term “antisense” nucleic acidmolecule is a nucleotide sequence that is complementary to its target.Preferably, an antisense sequence is constructed by inverting a regionpreceding or targeting the initiation codon or an unconserved region. Inanother embodiment the antisense sequence targets all or part of themRNA or cDNA of P450RAI-2. In particular, the nucleic acid sequencescontained in the nucleic acid molecules of the invention or a fragmentthereof may be inverted relative to its normal presentation fortranscription to produce antisense nucleic acid molecules. In oneembodiment the antisense molecules can be used to inhibit P450RAI-2expression and/or RA metabolism,

The antisense nucleic acid molecules of the invention or a fragmentthereof, may be chemically synthesized using naturally occurringnucleotides or variously modified nucleotides designed to increase thebiological stability of the molecules or to increase the physicalstability of the duplex formed with mRNA or the native gene e.g.phosphorothioate derivatives and acridine substituted nucleotides. Theantisense sequences may be produced biologically using an expressionvector introduced into cells in the form of a recombinant plasmid,phagemid or attenuated virus in which antisense sequences are producedunder the control of a high efficiency regulatory region, the activityof which may be determined by the cell type into which the vector isintroduced.

The invention also provides nucleic acids encoding fusion proteinscomprising a novel protein of the invention and a selected protein, or aselectable marker protein (see below).

II. Polypeptides of the Invention

The invention further contemplates an isolated P450RAI-2 protein. In anembodiment of the invention, an isolated protein is provided which hasthe human amino acid sequence as shown in SEQ ID NO:5 or a fragment,preferably biologically active fragment, thereof. The present inventionalso encompasses peptides encoded by the nucleic acid sequence of SEQ IDNO: 4 and all embodiments therefor as described in reference to thepeptides in SEQ ID NO. 5 described below.

Within the context of the present invention, a protein of the inventionmay in one embodiment include various structural forms of the primaryprotein which retain biological activity of the cytochrome P450RAI-2.For example, a protein of the invention may be in the form of acidic orbasic salts or in neutral form. In addition, individual amino acidresidues may be modified by oxidation or reduction. The biologicalactivity of a active cytochrome P450RAI-2 is the ability to oxidize aretinoid. Such activity can be tested for as described herein.

In addition to the full length amino acid sequence (SEQ ID NO: 5), theproteins of the present invention may also include truncations of theproteins, and analogs, and homologs of the proteins and truncationsthereof as described herein. Truncated proteins may comprise peptides ofat least 10 and preferably at least fourteen amino acid residues.

In one embodiment, the invention provides a peptide fragment of humanSEQ ID NO: 5. In another embodiment the invention provides a peptidehaving an amino acid sequence of the partial mouse P450RAI-2 sequence,SEQ ID NO: 11 or Zebrafish sequence (SEQ ID NO: 12). In anotherembodiment the invention provides a peptide encoded by any of thenucleic acid molecules of the invention as described above. In yetanother embodiment the invention provides an antigenic immunogenicfragment of the proteins of the invention.

Analogs of the proteins having the amino acid sequences shown in SEQ IDNO: 5 and/or truncations thereof as described herein, may include, butare not limited to an amino acid sequence containing one or more aminoacid substitutions, insertions, and/or deletions. Amino acidsubstitutions may be of a conserved or non-conserved nature. Conservedamino acid substitutions involve replacing one or more amino acids ofthe proteins of the invention with amino acids of similar charge, size,and/or hydrophobicity characteristics. When only conserved substitutionsare made the resulting analog should be functionally equivalent.Non-conserved substitutions involve replacing one or more amino acids ofthe amino acid sequence with one or more amino acids which possessdissimilar charge, size, and/or hydrophobicity characteristics.

Without the intention of being limited thereby, in one embodiment it ispreferable that substitutions of amino acids are made that preserve thestructure responsible for retinoid metabolizing activity of the proteinsdisclosed herein. Conservative substitutions are described in the patentliterature, as for example, in U.S. Pat. No. 5,264,558. It is thusexpected, for example, that interchange among non-polar aliphaticneutral amino acids, glycine, alanine, proline, valine and isoleucine,would be possible. Likewise, substitutions among the polar aliphaticneutral amino acids, serine, threonine, methionine, asparagine andglutamine could possibly be made. Substitutions among the charged acidicamino acids, aspartic acid and glutamic acid, could probably be made, ascould substitutions among the charged basic amino acids, lysine andarginine. Substitutions among the aromatic amino acids, includingphenylalanine, histidine, tryptophan and tyrosine would also likely bepossible. These sorts of substitutions and interchanges are well knownto those skilled in the art. Other substitutions might well be possible.Of course, it would also be expected that the greater the percentage ofhomology, i.e., sequence similarity, of a variant protein with anaturally occurring protein, the greater the retention of metabolicactivity. Of course, as protein variants having the activity ofP450RAI-2 as described herein are intended to be within the scope ofthis invention, so are nucleic acids encoding such variants.

One or more amino acid insertions may be introduced into the amino acidsequences shown in SEQ ID NO: 5. Amino acid insertions may consist ofsingle amino acid residues or sequential amino acids ranging from 2 to15 amino acids in length. For example, amino acid insertions may be usedto destroy target sequences so that the protein is no longer active.This procedure may be used in vivo to inhibit the activity of a proteinof the invention.

Deletions may consist of the removal of one or more amino acids, ordiscrete portions from the amino acid sequence shown in SEQ ID NO: 5.The deleted amino acids may or may not be contiguous. The lower limitlength of the resulting analog with a deletion mutation is about 10amino acids, preferably 100 amino acids.

Analogs of the proteins of the invention may be prepared by introducingmutations in the nucleotide sequence encoding the protein. Mutations innucleotide sequences constructed for expression of analogs of a proteinof the invention must preserve the reading frame of the codingsequences. Furthermore, the mutations will preferably not createcomplementary regions that could hybridize to produce secondary mRNAstructures, such as loops or hairpins, which could adversely affecttranslation of the mRNA.

Mutations may be introduced at particular loci by synthesizingoligonucleotides containing a mutant sequence, flanked by restrictionsites enabling ligation to fragments of the native sequence. Followingligation, the resulting reconstructed sequence encodes an analog havingthe desired amino acid insertion, substitution, or deletion.

Alternatively, oligonucleotide-directed site specific mutagenesisprocedures may be employed to provide an altered gene having particularcodons altered according to the substitution, deletion, or insertionrequired. Deletion or truncation of a protein of the invention may alsobe constructed by utilizing convenient restriction endonuclease sitesadjacent to the desired deletion. Subsequent to restriction, overhangsmay be filled in, and the DNA religated. Exemplary methods of making thealterations set forth above are disclosed by Sambrook et al (MolecularCloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor LaboratoryPress, 1989).

Insertions, deletions or substitution mutations of P450RAI-2 can be usedto generate dominant negative forms of P450RAI-2 that can act astransdominant repressors of P450RAI-2 activity.

The proteins of the invention also include homologs of the amino acidsequence shown in SEQ ID NO: 5 and/or truncations thereof as describedherein. Such homologs are proteins whose amino acid sequences areencoded by nucleic acid sequences that hybridize under stringenthybridization conditions (see discussion of stringent hybridizationconditions herein) with a probe used to obtain a protein of theinvention. Homologs of a protein of the invention will have the sameregions which are characteristic of the protein.

A homologous protein includes a protein with an amino acid sequencehaving at least 60%, preferably at least 76%, preferably 80-90% identitywith the amino acid sequence as shown in SEQ ID NO: 5.

The invention also contemplates isoforms of the proteins of theinvention. An isoform contains the same number and kinds of amino acidsas a protein of the invention, but the isoform has a different molecularstructure. The isoforms contemplated by the present invention are thosehaving the same properties as a protein of the invention as describedherein.

The present invention also includes a protein of the inventionconjugated with a selected protein, or a selectable marker protein (seebelow) to produce fusion proteins. Additionally, immunogenic portions ofa protein of the invention are within the scope of the invention.Immunogenic portions of a protein is that portion that if administeredto a patient can induce an immune response and preferably an antibodyresponse.

A further advantage may be obtained through chimeric forms of theprotein, as known in the art. A DNA sequence encoding the entireprotein, or a portion of the protein, could thus be linked, for example,with a sequence coding for the C-terminal portion of E. coliβ-galactosidase to produce a fusion protein. GST-P450RAI-2 fusionproteins are described in the above examples. An expression system forhuman respiratory syncytial virus glycoproteins F and G is described inU.S. Pat. No. 5,288,630 issued Feb. 22, 1994 and references citedtherein, for example.

The proteins of the invention (including truncations, analogs, etc.) maybe prepared using recombinant DNA methods. These proteins may bepurified and/or isolated to various degrees using techniques known inthe art. Accordingly, nucleic acid molecules of the present inventionhaving a sequence which encodes a protein of the invention may beincorporated according to procedures known in the art into anappropriate expression vector which ensures good expression of theprotein. Possible expression vectors include but are not limited tocosmids, plasmids, or modified viruses (e.g., replication defectiveretroviruses, adenoviruses and adeno-associated viruses), so long as thevector is compatible with the host cell used. The expression “vectorssuitable for transformation of a host cell”, means that the expressionvectors contain a nucleic acid molecule of the invention and regulatorysequences, selected on the basis of the host cells to be used forexpression, which are operatively linked to the nucleic acid molecule.“Operatively linked” is intended to mean that the nucleic acid is linkedto regulatory sequences in a manner which allows expression of thenucleic acid.

The invention therefore contemplates a recombinant expression vector ofthe invention containing a nucleic acid molecule of the invention, or afragment thereof, and the necessary regulatory sequences for thetranscription and translation of the inserted protein-sequence. Suitableregulatory sequences may be derived from a variety of sources, includingbacterial, fungal, or viral genes (For example, see the regulatorysequences described in Goeddel, Gene Expression Technology: Methods inEnzymology 185, Academic Press, San Diego, Calif. (1990). Selection ofappropriate regulatory sequences is dependent on the host cell chosen,and may be readily accomplished by one of ordinary skill in the art.Examples of such regulatory sequences include: a transcriptionalpromoter and enhancer or RNA polymerase binding sequence, a ribosomalbinding sequence, including a translation initiation signal.Additionally, depending on the host cell chosen and the vector employed,other sequences, such as an origin of replication, additional DNArestriction sites, enhancers, and sequences conferring inducibility oftranscription may be incorporated into the expression vector. It willalso be appreciated that the necessary regulatory sequences may besupplied by the native protein and/or its flanking regions.

The invention further provides a recombinant expression vectorcomprising a DNA nucleic acid molecule of the invention cloned into theexpression vector in an antisense orientation. That is, the DNA moleculeis operatively linked to a regulatory sequence in a manner which allowsfor expression, by transcription of the DNA molecule, of an RNA moleculewhich is antisense to a nucleotide sequence of the invention preferablycomprising the nucleotides as shown in SEQ ID NO: 4 or fragmentsthereof. Regulatory sequences operatively linked to the antisensenucleic acid can be chosen which direct the continuous expression of theantisense RNA molecule.

The recombinant expression vectors of the invention may also contain aselectable marker gene that facilitates the selection of host cellstransformed or transfected with a recombinant molecule of the invention.Examples of selectable marker genes are genes encoding a protein whichconfers resistance to certain drugs, such as G418 and hygromycin.Examples of other markers which can be used are: green fluorescentprotein (GFP), β-galactosidase, chloramphenicol acetyltransferase, orfirefly luciferase. Transcription of the selectable marker gene ismonitored by changes in the concentration of the selectable markerprotein such as β-galactosidase, chloramphenicol acetyltransferase, orfirefly luciferase. If the selectable marker gene encodes a proteinconferring antibiotic resistance such as neomycin resistancetransformant cells can be selected with G418. Cells that haveincorporated the selectable marker gene will survive, while the othercells die. This makes it possible to visualize and assay for expressionof recombinant expression vectors of the invention and in particular todetermine the effect of a mutation on expression and phenotype. It willbe appreciated that selectable markers can be introduced on a separatevector from the nucleic acid of interest.

The recombinant expression or cloning vectors of the invention may alsocontain genes which encode a fusion moiety which provides increasedexpression of the recombinant protein; increased solubility of therecombinant protein; and aid in the purification of a target recombinantprotein by acting as a ligand in affinity purification. For example, aproteolytic cleavage site may be added to the target recombinant proteinto allow separation of the recombinant protein from the fusion moietysubsequent to purification of the fusion protein.

Recombinant expression vectors can be introduced into host cells toproduce a transformed host cell. The term “transformed host cell” isintended to include prokaryotic and eukaryotic cells which have beentransformed or transfected with a recombinant expression vector of theinvention. The terms “transformed with”, “transfected with”,“transformation” and “transfection” are intended to encompassintroduction of nucleic acid (e.g. a vector) into a cell by one of manypossible techniques known in the art. Prokaryotic cells can betransformed with nucleic acid by, for example, electroporation orcalcium chloride mediated transformation. Nucleic acid can be introducedinto mammalian cells via conventional techniques such as calciumphosphate or calcium chloride co precipitation, DEAE-dextran-mediatedtransfection, lipofectin, electroporation or microinjection. Suitablemethods for transforming and transfecting host cells can be found inSambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition,Cold Spring Harbor Laboratory press (1989)), and other such laboratorytextbooks.

Suitable host cells include a wide variety of prokaryotic and eukaryotichost cells. For example, the proteins of the invention may be expressedin bacterial cells such as E. coli, insect cells (using baculovirus),yeast cells or mammalian cells, COS1 cells. Other suitable host cellscan be found in Goeddel, Gene Expression Technology: Methods inEnzymology 185, Academic Press, San Diego, Calif. (1991).

The invention includes a microbial cell that contains and is capable ofexpressing a heterologous a nucleic acid molecule having a nucleotidesequence as broadly encompassed by the invention. The heterologousnucleic acid molecule can be DNA.

Isolated DNA of the invention can be contained in a recombinant cloningvector.

The invention includes a stably transfected cell line which expressesany one or more proteins as broadly defined by the invention.

The invention includes a culture of cells transformed with a recombinantDNA molecule having a nucleotide sequence as broadly encompassed by theinvention. Such a culture of cells can be eukaryotic. They can bepiscine—particularly zebrafish, mammalian—particularly human, rat ormouse, for example.

The invention is also a process for producing any protein as broadlydefined by the invention. The process includes such steps as:

-   -   preparing a DNA fragment including a nucleotide sequence which        encodes said protein;    -   incorporating the DNA fragment into an expression vector to        obtain a recombinant DNA molecule which includes the DNA        fragment and is capable of undergoing replication;    -   transforming a host cell with said recombinant DNA molecule to        produce a transformant which can express said protein;    -   culturing the transformant to produce said protein; and    -   recovering said protein from resulting cultured mixture.

More particularly, the invention provides a method of preparing apurified protein of the invention comprising introducing into a hostcell a recombinant nucleic acid encoding the protein, allowing theprotein to be expressed in the host cell and isolating and purifying theprotein. Preferably, the recombinant nucleic acid is a recombinantexpression vector. Proteins can be isolated from a host cell expressingthe protein and purified according to standard procedures of the art,including ammonium sulfate precipitation, column chromatography (e.g.ion exchange, gel filtration, affinity chromatography, etc.),electrophoresis, and ultimately, crystallization [see generally, “EnzymePurification and Related Techniques”, Methods in Enzymology, 22, 233-577(1971)].

Alternatively, the protein or parts thereof can be prepared by chemicalsynthesis using techniques well known in the chemistry of proteins suchas solid phase synthesis [Merrifield 1964] or synthesis in homogeneoussolution [Houbenwycl, 1987].

III. Applications

1. Diagnostic Applications

The above nucleic acid and peptide molecules of the invention can beused to diagnose a disease affected by P450RAI-2 expression, such as adisease or medical condition associated with or where RA, P450RAI-2 orinhibitors thereof treatment may be indicated. Examples of suchconditions have been outlined herein, such as diseases associated withangiogenesis the regulation of the cell cycle or apoptosis, such ascancer, dysplasia, various autoimmune diseases. Determination of peptideor nucleic acid expression levels could assist not only in identifying amedical condition but in determining the appropriate course oftreatment.

(i) Nucleic Acids

The above described nucleic acid molecules of the invention, allow thoseskilled in the art to construct nucleotide probes for use in thedetection of nucleotide sequences homologous to P450RAI-2 or a fragmentthereof in a sample.

Accordingly, the present invention also relates to a method of detectingthe presence of nucleic acid molecules encoding a P450RAI-2 in a samplecomprising contacting the sample under hybridization conditions with oneor more nucleotide probes which hybridize to the nucleic acid moleculesand are labelled with a detectable marker, and, determining the degreeof hybridization between the nucleic acid molecule in the sample and thenucleotide probe(s).

A nucleotide probe may be labelled with a detectable marker such as aradioactive label which provides for an adequate signal and hassufficient half life such as 32P, 3H, 14C or the like. Other detectablemarkers which may be used include antigens that are recognized by aspecific labelled antibody, fluorescent compounds, enzymes, antibodiesspecific for a labelled antigen, and chemiluminescent compounds. Anappropriate label may be selected having regard to the rate ofhybridization and binding of the probe to the nucleotide to be detectedand the amount of nucleotide available for hybridization.

Hybridization conditions which may be used in methods of the inventionare known in the art and are described for example in Sambrook J, FritchE F, Maniatis T. In: Molecular Cloning, A Laboratory Manual, 1989.(Nolan C, Ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y. The hybridization product may be assayed using techniques known inthe art. The nucleotide probe may be labelled with a detectable markeras described herein and the hybridization product may be assayed bydetecting the detectable marker or the detectable change produced by thedetectable marker.

A nucleic acid molecule of the invention also permits the identificationand isolation, or synthesis of nucleotide sequences which may be used asprimers to amplify a nucleic acid molecule of the invention, forexample, in a polymerase chain reaction (PCR) which is discussed in moredetail below. The primers may be used to amplify the genomic DNA or mRNAof other P450RAI-2 genes or coding sequences. The PCR amplifiedsequences can be examined to determine the relationship between thevarious P450RAI-2 genes.

The length and bases of primers for use in a PCR are selected so thatthey will hybridize to different strands of the desired sequence and atrelative positions along the sequence such that an extension productsynthesized from one primer when it is separated from its template canserve as a template for extension of the other primer into a nucleicacid of defined length. Primers which may be used in the invention areoligonucleotides, i.e., molecules containing two or moredeoxyribonucleotides of the nucleic acid molecule of the invention whichoccur naturally as in a purified restriction endonuclease digest or areproduced synthetically using techniques known in the art such as forexample phosphotriester and phosphodiester methods (See Good et al.Nucl. Acid Res 4:2157, 1977) or automated techniques (See for example,Conolly, B. A. Nucleic Acids Res. 15:15(7): 3131, 1987). The primers arecapable of acting as a point of initiation of synthesis when placedunder conditions which permit the synthesis of a primer extensionproduct which is complementary to a DNA sequence of the invention, i.e.,in the presence of nucleotide substrates, an agent for polymerizationsuch as DNA polymerase and at suitable temperature and pH. Preferably,the primers are sequences that do not form secondary structures by basepairing with other copies of the primer or sequences that form a hairpin configuration. The primer preferably contains between about 7 and 25nucleotides.

The primers may be labelled with detectable markers which allow fordetection of the amplified products. Suitable detectable markers areradioactive markers such as P-32, S-35, I-125, and H-3, luminescentmarkers such as chemiluminescent markers, preferably luminol, andfluorescent markers, preferably dansyl chloride,fluorcein-5-isothiocyanate, and 4-fluor-7-nitrobenz-2-axa-1,3 diazole,enzyme markers such as horseradish peroxidase, alkaline phosphatase,β-galactosidase, acetylcholinesterase, or biotin.

It will be appreciated that the primers may contain non-complementarysequences provided that a sufficient amount of the primer contains asequence which is complementary to a nucleic acid molecule of theinvention or oligonucleotide fragment thereof, which is to be amplified.Restriction site linkers may also be incorporated into the primersallowing for digestion of the amplified products with the appropriaterestriction enzymes facilitating cloning and sequencing of the amplifiedproduct.

In an embodiment of the invention a method of determining the presenceof a nucleic acid molecule having a sequence encoding a protein of theinvention is provided comprising treating the sample with primers whichare capable of amplifying the nucleic acid molecule or a predeterminedoligonucleotide fragment thereof in a polymerase chain reaction to formamplified sequences, under conditions which permit the formation ofamplified sequences and, assaying for amplified sequences.

Polymerase chain reaction as used herein refers to a process foramplifying a target nucleic acid sequence as generally described inInnis et al, Academic Press, 1990 in Mullis et al., U.S. Pat. No.4,863,195 and Mullis, U.S. Pat. No. 4,683,202. Conditions for amplifyinga nucleic acid template are described in M. A. Innis and D. H. Gelfand,PCR Protocols, A Guide to Methods and Applications M. A. Innis, D. H.Gelfand, J. J. Sninsky and T. J. White eds, pp 3-12, Academic Press1989.

The amplified products can be isolated and distinguished based on theirrespective sizes using techniques known in the art. For example, afteramplification, a DNA sample can be separated on an agarose gel andvisualized, after staining with ethidium bromide, under ultra violet(uv) light. DNA may be amplified to a desired level and a furtherextension reaction may be performed to incorporate nucleotidederivatives having detectable markers such as radioactive labelled orbiotin labelled nucleoside triphosphates. The primers may also belabelled with detectable markers as discussed above. The detectablemarkers may be analyzed by restriction enzyme digestion andelectrophoretic separation or other techniques known in the art.

Conditions which may be employed in the methods of the invention usingPCR are those which permit hybridization and amplification reactions toproceed in the presence of DNA in a sample and appropriate complementaryhybridization primers. Conditions suitable for a polymerase chainreaction are generally known in the art. For example, see M. A. Innisand D. H. Gelfand, PCR Protocols, A guide to Methods and Applications M.A. Innis, D. H. Gelfand, J. J. Sninsky and T. J. White eds, pp 3-12,Academic Press 1989. To amplify DNA template strands, preferably, thePCR utilizes polymerase obtained from the thermophilic bacterium Thermusaquatics (Taq polymerase, GeneAmp Kit, Perkin Elmer Cetus) or otherthermostable polymerase.

It will be appreciated that other techniques such as the Ligase ChainReaction (LCR) and NASBA may be used to amplify a nucleic acid moleculeof the invention (Barney in “PCR Methods and Applications”, August 1991,Vol. 1(1), page 5, and European Published Application No. 0320308,published Jun. 14, 1989, and U.S. Pat. No. 5,130,238 to Malek).

(ii) Antibodies

A P450RAI-2 protein of the invention or antigenic portion thereof can beused to prepare antibodies specific for the proteins of the invention,preferably to a protein having SEQ ID NO: 5 or partial sequence SEQ IDNO: 11 or 12. Antibodies can be prepared which bind a distinct epitopein an unconserved region of the protein. An unconserved region of theprotein is one which does not have substantial sequence homology toother proteins. Alternatively, a region from a well-characterized domaincan be used to prepare an antibody to a conserved region of a protein ofthe invention. Antibodies having specificity for a protein of theinvention may also be raised from fusion proteins.

Conventional methods can be used to prepare the antibodies. For example,by using a peptide of a protein of the invention, polyclonal antisera ormonoclonal antibodies can be made using standard methods. A mammal,(e.g., a mouse, hamster, or rabbit) can be immunized with an immunogenicform of the peptide which elicits an antibody response in the mammal.Techniques for conferring immunogenicity on a peptide includeconjugation to carriers or other techniques well known in the art. Forexample, the peptide can be administered in the presence of adjuvant.The progress of immunization can be monitored by detection of antibodytiters in plasma or serum. Standard ELISA or other immunoassayprocedures can be used with the immunogen as antigen to assess thelevels of antibodies. Following immunization, antisera can be obtainedand, if desired, polyclonal antibodies isolated from the sera.

To produce monoclonal antibodies, antibody producing cells (lymphocytes)can be harvested from an immunized animal and fused with myeloma cellsby standard somatic cell fusion procedures thus immortalizing thesecells and yielding hybridoma cells. Such techniques are well known inthe art, (e.g., the hybridoma technique originally developed by Kohlerand Milstein (Nature 256, 495-497 (1975)) as well as other techniquessuch as the human B-cell hybridoma technique (Kozbor et al., Immunol.Today 4, 72 (1983)); the EBV-hybridoma technique to produce humanmonoclonal antibodies (Cole et al. Monoclonal Antibodies in CancerTherapy (1985) Allen R. Bliss, Inc., pages 77-96); and screening ofcombinatorial antibody libraries (Huse et al., Science 246, 1275(1989)). Hybridoma cells can be screened immunochemically for productionof antibodies specifically reactive with the peptide and the monoclonalantibodies can be isolated. Therefore, the invention also contemplateshybridoma cells secreting monoclonal antibodies with specificity for aprotein of the invention.

The term “antibody” as used herein is intended to include fragmentsthereof which also specifically react with, a protein of the invention,or peptide thereof. Antibodies can be fragmented using conventionaltechniques and the fragments screened for utility in the same manner asdescribed above. For example, F(ab′)2 fragments can be generated bytreating antibody with pepsin. The resulting F(ab′)2 fragment can betreated to reduce disulfide bridges to produce Fab′ fragments.

Chimeric antibody derivatives, i.e., antibody molecules that combine anon-human animal variable region and a human constant region are alsocontemplated within the scope of the invention. Chimeric antibodymolecules can include, for example, the antigen binding domain from anantibody of a mouse, rat, or other species, with human constant regions.Conventional methods may be used to make chimeric antibodies containingthe immunoglobulin variable region which recognizes a P450RAI-2 proteinof the invention (See, for example, Morrison et al., Proc. Natl. Acad.Sci. U.S.A. 81,6851 (1985); Takeda et al., Nature 314, 452 (1985),Cabilly et al., U.S. Pat. No. 4,816,567; Boss et al., U.S. Pat. No.4,816,397; Tanaguchi et al., European Patent Publication EP171496;European Patent Publication 0173494, United Kingdom patent GB 2177096B).

Monoclonal or chimeric antibodies specifically reactive with a proteinof the invention as described herein can be further humanized byproducing human constant region chimeras, in which parts of the variableregions, particularly the conserved framework regions of theantigen-binding domain, are of human origin and only the hypervariableregions are of non-human origin. Such immunoglobulin molecules may bemade by techniques known in the art (e.g., Teng et al., Proc. Natl.Acad. Sci. U.S.A., 80, 7308-7312 (1983); Kozbor et al., ImmunologyToday, 4, 7279 (1983); Olsson et al., Meth. Enzymol., 92, 3-16 (1982);and PCT Publication WO92/06193 or EP 0239400). Humanized antibodies canalso be commercially produced (Scotgen Limited, 2 Holly Road,Twickenham, Middlesex, Great Britain.)

Specific antibodies, or antibody fragments reactive against a protein ofthe invention may also be generated by screening expression librariesencoding immunoglobulin genes, or portions thereof, expressed inbacteria with peptides produced from nucleic acid molecules of thepresent invention. For example, complete Fab fragments, VH regions andFV regions can be expressed in bacteria using phage expression libraries(See for example Ward et al., Nature 341, 544-546: (1989); Huse et al.,Science 246, 1275-1281 (1989); and McCafferty et al. Nature 348, 552-554(1990)).

The antibodies may be labelled with a detectable marker includingvarious enzymes, fluorescent materials, luminescent materials andradioactive materials. Examples of suitable enzymes include horseradishperoxidase, alkaline phosphatase, β-galactosidase, oracetylcholinesterase; examples of suitable fluorescent materials includeumbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine,dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; anexample of a luminescent material includes luminol; and examples ofsuitable radioactive material include S-35, Cu-64, Ga-67, Zr-89, Ru-97,Tc-99m, Rh-105, Pd-109, In-111, I-123, I-125, I-131, Re-186, Au-198,Au-199, Pb-203, At-211, Pb-212 and Bi-212. The antibodies may also belabelled or conjugated to one partner of a ligand binding pair.Representative examples include avidin-biotin and riboflavin-riboflavinbinding protein. Methods for conjugating or labelling the antibodiesdiscussed above with the representative labels set forth above may bereadily accomplished using conventional techniques.

Antibodies reactive against P450RAI-2 proteins of the invention (e.g.,enzyme conjugates or labelled derivatives) may be used to detect aprotein of the invention in various samples, for example they may beused in any known immunoassays which rely on the binding interactionbetween an antigenic determinant of a protein of the invention and theantibodies. Examples of such assays are radioimmunoassays, westernimmunoblotting, enzyme immunoassays (e.g., ELISA), immunofluorescence,immunoprecipitation, latex agglutination, hemagglutination, andhistochemical tests. Thus, the antibodies may be used to identify orquantify the amount of a protein of the invention in a sample.

A sample may be tested for the presence or absence of a P450RAI-2 bycontacting the sample with an antibody specific for an epitope of aP450RAI-2 protein which antibody is capable of being detected after itbecomes bound to a P450RAI-2 protein in the sample, and assaying forantibody bound to a P450RAI-2 protein in the sample, or unreactedantibody.

In a method of the invention a predetermined amount of a sample orconcentrated sample is mixed with antibody or labelled antibody. Theamount of antibody used in the method is dependent upon the labellingagent chosen. The resulting protein bound to antibody or labelledantibody may be isolated by conventional isolation techniques, forexample, salting out, chromatography, electrophoresis, gel filtration,fractionation, absorption, polyacrylamide gel electrophoresis,agglutination, or combinations thereof.

The sample or antibody may be insolubilized, for example, the sample orantibody can be reacted using known methods with a suitable carrier.Examples of suitable carriers are Sepharose or agarose beads. When aninsolubilized sample or antibody is used protein bound to antibody orunreacted antibody is isolated by washing. For example, when the sampleis blotted onto a nitrocellulose membrane, the antibody bound to aprotein of the invention is separated from the unreacted antibody bywashing with a buffer, for example, phosphate buffered saline (PBS) withbovine serum albumin (BSA).

When labelled antibody is used, the presence of a P450RAI-2 can bedetermined by measuring the amount of labelled antibody bound to aprotein of the invention in the sample or of the unreacted labelledantibody. The appropriate method of measuring the labelled material isdependent upon the labelling agent.

When unlabelled antibody is used in a method of the invention, thepresence of a P450RAI-2 can be determined by measuring the amount ofantibody bound to the P450RAI-2 using substances that interactspecifically with the antibody to cause agglutination or precipitation.In particular, labelled antibody against an antibody specific for aprotein of the invention, can be added to the reaction mixture. Theantibody against an antibody specific for a protein of the invention canbe prepared and labelled by conventional procedures known in the artwhich have been described herein. The antibody against an antibodyspecific for a protein of the invention may be a species specificanti-immunoglobulin antibody or monoclonal antibody, for example, goatanti-rabbit antibody may be used to detect rabbit antibody specific fora protein of the invention.

(iii) Methods of the Invention

The invention includes a protein of the invention for use inmetabolizing retinoic acid in an organism or cell in need of suchmetabolizing. The invention also includes use of a protein of theinvention in the preparation of a medicament for use in metabolizingretinoic acid in an organism. Preferably the protein has sequence of SEQID NO: 5.

The invention includes a method for metabolizing retinoic acid,particularly all-trans retinoic acid, in an organism or cell comprisingadministering a protein as broadly defined by the invention, mostpreferably of SEQ ID NO: 5.

The invention is also a method for inhibiting retinoic acidhydroxylation in an organism in need of such inhibition, comprisingadministering to the organism an effective amount of an antisensenucleic acid or oligonucleotide substantially complementary to at leasta portion of the sequence identified as SEQ ID NO:4. In such a method,the portion can be at least 5 bases in length, or at least about 10bases in length, or at least about 15 bases in length, or at least about20 bases in length, or at least about 25 bases in length, or at leastabout 30 bases in length, or at least about 35 bases in length, or atleast about 40 bases in length, or at least about 45 bases in length, orat least about 50 bases in length. Other inhibitors, of RA metabolismsuch as antibodies to P450RAI-2, or inhibitors of P450RAI-2 activitycould also be used.

A preferred organism to be treated is human but could be any organismwith an RA metabolism or P450RAI-2 related condition.

The organism may be being treated for a medical condition or diseasewherein RA treatment may be indicated. In one embodiment the disease ormedical condition is selected from the group consisting of cancer,angiogenesis, actinic keratosis, oral leukoplakia, a secondary tumor ofthe head and/or neck, a non-small cell lung carcinoma, a basal cellcarcinoma, acute promyelocytic leukemia, skin cancer, and apremalignancy associated actinic keratosis, acne, psoriasis and/orichthyosis, and particularly, acute promyelocytic leukemia. In anotherembodiment the peptides and nucleic and molecules of the invention maybe used to treat disorders of the brain such as memory loss or learningdificiencies.

In one embodiment the invention includes a kit for determining thepresence of a protein as broadly described above, or containing an aminoacid sequence as identified by SEQ ID NO:5 (human P450RAI-2) SEQ IDNO:11 (mouse CYP26B) or SEQ ID NO:12 (zebrafish CYB26B), comprising anantibody to the protein linked to a reporter system, wherein thereporter system produces a detectable response when a predeterminedamount of the protein and the antibody are bound together. In apreferred aspect, the antibody is specific for a protein that includesthe amino acid sequence identified as SEQ ID NO:5.

The invention also includes a kit for determining the presence of afirst said nucleic acid molecule as broadly defined by the invention.The kit includes a second nucleic acid molecule capable of hybridizingwith at least a portion of a the first nucleic acid molecule under thehigh stringency conditions of paragraph (a), above, in which the secondnucleic acid molecule is linked to a reporter system wherein thereporter system produces a detectable response when a predeterminedamount of the first and second molecules are hybridized together. Thesecond nucleic acid molecule can be at least 5 bases in length, or atleast about 10 bases in length, or at least about 15 bases in length, orat least about 20 bases in length, or at least about 25 bases in length,or at least about 30 bases in length, or at least about 35 bases inlength, or at least about 40 bases in length, or at least about 45 basesin length, or at least about 50 bases in length.

The invention is also a method of screening drugs for their modulatingeffect on activity of a protein as broadly defined by the invention,which method includes exposing a purified said protein to a said drugand determining the effect on the activity. Usually, the modulatingeffect would be to inhibit the activity of the protein in question.Typically, the activity of the protein is oxidation, e.g., hydroxylationof a retinoic acid, particularly all-trans retinoic acid. In a preferredembodiment, the activity is oxidation of all-trans retinoic acid and theprotein includes the amino identified as SEQ ID NO:5.

The invention also includes a method of screening drugs for their effecton expression of a gene, wherein the gene is an inducible genecontaining a nucleotide sequence as broadly defined by the invention, byall-trans retinoic acid. The method includes exposing a eukaryotic cellto a said drug and determining the effect on gene expression.Preferably, the gene includes the nucleotide sequence identified as SEQID NO:4.

The cell can be a mammalian cell, particularly, a human cell.

The invention includes any drug identified according to a method of theinvention, particularly for a purpose related to its related to itsmodulating effect on the activity of a protein of the invention.

The invention includes a method for inhibiting retinoic acid metabolismin an organism in need of such inhibition, or in cells obtained fromsuch an organism, comprising administering to the organism an effectiveamount of a drug of the invention.

The invention includes a method of oxidizing a retinoid. The methodincludes exposing the retinoid to a protein as broadly defined by theinvention, and particularly where the protein includes the amino acidsequence identified as SEQ ID NO:5. The retinoid can be a retinoic acid,particularly, all-trans retinoic acid.

In another aspect, the invention is a method of screening a drug for itsactivity on a protein. The method includes steps of:

-   -   (i) providing a cell line having heterologous DNA encoding a        functional protein as broadly defined by the invention        incorporated thereinto so as to be capable of expressing said        protein;    -   (ii) exposing the cell line to the drug under conditions in        which said protein is expressed in an active form to expose the        protein to the drug; and    -   (iii) determining the effect of the drug on the activity of the        protein.

The method can include exposing the cell line to a substrate of theprotein under conditions in which the protein is expressed in an activeform to expose the protein to the substrate.

In a particular aspect, the activity is oxidation.

Step (ii) of the method can include exposing the cell line to the drugand the substrate simultaneously.

The substrate can be a retinoid, particularly, a retinoic acid, moreparticularly, all-trans retinoic acid.

The oxidative activity can be oxidation of the β-ionone ring of thesubstrate, particularly, hydroxylation.

According to a particular aspect, the heterologous DNA encodes theprotein identified as SEQ ID NO:5.

The invention is also a method for screening an agent for its effect onan activity of a first protein relative to its effect on the activity ofa second protein. This method includes steps of:

-   -   (a) providing a first protein, wherein the protein one defined        according this invention;    -   (b) providing a second protein, wherein the second protein is a        cytochrome P450;    -   (c) exposing the first protein to the agent;    -   (d) exposing the second protein to the agent; and    -   (e) determining the effect of the agent on the activity of the        first protein relative to its effect on the activity of the        second protein.

According to the method, the activity of each protein underconsideration can be the ability of the proteins to oxidize a retinoidand it optionally limited to the ability to oxidize a retinoid at the4-position of the β-ionone ring and/or to hydroxylate a retinoid at the4-position of the β-ionone ring.

The retinoid can be a retinoic acid, and it can simply be all-transretinoic acid.

The first protein can be a human protein and it can include the sequenceidentified as SEQ ID NO:5.

The method can be such that the second protein is selected from thegroup of proteins encoded by: (a) a nucleotide sequence that hybridizesunder high stringency conditions, wherein high stringency conditionsinclude a wash step of about 0.2×SSC at 50° C., to the nucleotidesequence shown as SEQ ID NO:13 or SEQ ID NO:14 or SEQ ID NO:17, andencodes a protein that oxidizes a retinoid; and (b) a nucleotidesequence that hybridizes under high stringency conditions, wherein highstringency conditions include a wash step of about 0.2×SSC at 50° C., tothe nucleotide sequence shown as SEQ ID NO:13 or SEQ ID NO:14, andencodes a protein that hydroxylates retinoic acid at the 4 position ofthe β-ionone ring.

The second protein can be a human protein and it can include a proteinwhich includes the amino acid sequence encoded by the nucleotidesequence identified as SEQ ID NO:13.

Step (c) of the method can include exposing the first protein to aretinoid.

Step (d) of the method can include exposing the second protein to aretinoid.

Each of steps (c) and (d) can include exposing the first protein to aretinoid.

Step (c) can include exposing the first protein to said retinoid atvarious concentrations and/or step (d) can include exposing the secondprotein to said retinoid at various concentrations.

In another broad aspect, the invention is a method for screening anagent for its effect on an activity of a first protein relative to itseffect on the activity of a second protein where the proteins are eachexpressed in a cell or group of cells. Such method thus includes:

-   -   (a) providing a group of first cells having expressibly        incorporated thereinto heterologous DNA encoding a first protein        wherein the protein is a protein of the invention as defined        herein;    -   (b) providing a group of second cells having expressibly        incorporated thereinto heterologous DNA encoding a second        protein, where the second protein is a cytochrome P450;    -   (c) exposing the first cells to the agent under conditions in        which the first protein is expressed;    -   (d) exposing the second cells to the agent under conditions in        which the second protein is expressed; and    -   (e) determining the effect of the agent on the activity of the        first protein relative to its effect on the activity of the        second protein.

Step (e) of the method can include monitoring the disappearance of theagent in the presence the first cells and monitoring the disappearanceof the agent in the presence of the second cells.

Step (e) can include monitoring the appearance of an oxidized product orproducts formed from the agent on exposure to the first cells andmonitoring the appearance of the oxidized product or products formedfrom the agent on exposure to the second cells.

Step (c) can include exposing the first cells to a substrate of thefirst protein in the presence of the agent and step (d) can includeexposing the second cells to the substrate in the presence of the agent.

Step (e) can include monitoring the production of a reaction product orproducts formed from the substrate on exposure to the first protein instep (c) and, further, step (e) can include monitoring the production ofthe reaction product or products formed from the substrate on exposureto the second protein in step (d).

Step (e) can include monitoring reduction in the amount of substrate onexposure to the first protein in step (c) and step (e) can includemonitoring the reduction in the amount of the substrate on exposure tothe second protein in step (d).

The substrate can be a retinoid, which can be a retinoic acid, which canbe all-trans retinoic acid.

The observed activity of each protein can be its ability to oxidize aretinoid, particularly, the ability to oxidize a retinoid at the4-position of the β-ionone ring, or the ability to hydroxylate aretinoid at the 4-position of the β-ionone ring.

The first protein can be a human protein and it can have the sequenceidentified as SEQ ID NO:5.

The second protein can be selected from the group of proteins encodedby: (a) a nucleotide sequence that hybridizes under high stringencyconditions, wherein high stringency conditions include a wash step ofabout 0.2×SSC at 50° C., to the nucleotide sequence shown as SEQ IDNO:13 or SEQ ID NO:14, and encodes a protein that oxidizes a retinoid;and (b) a nucleotide sequence that hybridizes under high stringencyconditions, wherein high stringency conditions include a wash step ofabout 0.2×SSC at 50° C., to the nucleotide sequence shown as SEQ IDNO:13 or SEQ ID NO:14, and encodes a protein that hydroxylates retinoicacid at the 4 position of the β-ionone ring.

The second protein can be a human protein and it can include the aminoacid sequence encoded by the nucleotide sequence identified as SEQ IDNO:13.

Step (c) of the method can include exposing the first cells to aretinoid.

Step (d) can include exposing the second cells to a retinoid.

Step (c) can include exposing the first cells to said retinoid atvarious concentrations.

Step (d) can also include exposing the second cells to a retinoid atvarious concentrations.

In another aspect, the present invention is a method of inducing in aneukaryotic cell, production of RNA comprising the nucleotide sequenceidentified as SEQ ID NO:4 The method includes the steps of:

-   -   exposing the cell to a retinoid; and    -   hybridizing the RNA with a probe comprising a nucleic acid        molecule comprising a nucleotide sequence which encodes a        protein of the present invention.

The cell can be a mammalian cell, particularly a human cell.

The retinoid can be a retinoic acid, particularly, all-trans retinoicacid.

The nucleic acid sequence can be a non-coding sequence complementary toa coding sequence of a nucleic acid molecule encoding the proteincomprising the amino acid sequence identified as SEQ ID NO: 5 and theprobe is at least 10 nucleotide residues in length, or the probe is atleast 15 nucleotide residues in length, or the probe is at least 20nucleotide residues in length, or the probe is at least 25 nucleotideresidues in length, or the probe is at least 30 nucleotide residues inlength, or the probe is at least 35 nucleotide residues in length, orthe probe is at least 40 nucleotide residues in length, or the probe isat least 45 nucleotide residues in length, or the probe is at least 50nucleotide residues in length, or the probe is at least 55 nucleotideresidues in length, or the probe is at least 56 nucleotide residues inlength, or the probe is at least 60 nucleotide residues in length.

The invention includes a method of inducing expression in an eukaryoticcell, a protein comprising the amino acid sequence identified as SEQ IDNO: 5, the method comprising the steps of:

-   -   exposing the cell to a retinoid in an amount sufficient to        induce said expression; and    -   isolating the protein from the cell.

Isolating the protein can include exposing proteins produced by the cellafter said exposure step to an antibody which binds specifically to thedesired protein.

In the context of this invention, an antibody which “specifically binds”(and grammatical equivalents) to a protein refers to the phenomenon inwhich an antibody recognizes and binds to a specific binding entity,e.g., protein, but substantially does not recognize or bind to any otherspecific binding entity.

The cell can be a mammalian cell, particularly, a human cell.

The retinoid can be a retinoic acid, particularly, all-trans retinoicacid.

Human genomic P450RAI-1 sequences are identified herein as SEQ ID NOs:15and 16. The mouse sequence encoding P450RAI-1 is identified herein asSEQ ID NO:17.

In another aspect, the present invention includes a fragment of thenucleotide sequence encoding P450RAI-2 (SEQ ID NO:4). Such a fragmentcan find usefulness as a probe. The complement of the probe can findutility in, for example, manufacture of the probe. In a particular use,the probe can be used to determine the presence of an RNA molecule in asample which might, or might not, also include an RNA molecule encodingP450RAI-1. Such a probe would generally be 20 nucleotides long or be atleast 20 nucleotides long. The probe could also be 25, 30, 35, 40, 45,50, 55, 60 or more nucleotides in length and the probe can include thefull length of the complement to the sequence to which it is intended tobind. The sequence of the probe would also be sufficientlydistinguishable from any portion of the sequence encoding P450RAI-1 thatit would not cross-hybridize to a significant extent to a nucleotidesequence that encodes P450RAI-1, or portion thereof, particularly to anRNA encoding P450RAI-1. Such a probe would thus be sufficientlydifferent from any sequence of contiguous nucleotides selected from thenucleotide sequence encoding human P450RAI-1 (SEQ ID NO:13) that thereis no more than about 60% homology between the two sequences when thetwo sequences are directly aligned with each other. More preferably, thepercent homology would be less than about 55%, or less than about 50%,or less than about 45%, or even less than about 40%. Certain probes ofthe invention are selected so as span borders between introns of thecoding sequence as determined from the genomic sequence (SEQ ID NO:3).

The invention includes the method determining the presence of a nucleicmolecule encoding P450RAI-2 in a sample containing RNA isolated fromhuman cell, using such a probe.

In the context of this specification, the term “conserved” describessimilarity between sequences. The degree of conservation between twosequences can be determined by optimally aligning the sequences forcomparison. Here, sequences were aligned using the Omiga softwareprogram, Version 1.13. (Oxford Molecular Group, Inc., Campbell, Calif.).The Omiga software uses the Clustal W Alignment algorithms [Higgins etal., 1989; Higgins et al., 1991; Thompson et al. 1994] Default settingsused are as follows: Open gap penalty 10.00; Extend gap penalty 0.05;Delay divergent sequence 40 and Scoring matrix—Gonnet Series. Percentidentity or homology between two sequences is determined by comparing aposition in the first sequence with a corresponding position in thesecond sequence. When the compared positions are occupied by the samenucleotide or amino acid, as the case may be, the two sequences areconserved at that position. The degree of conservation between twosequences is often expressed, as it is here, as a percentagerepresenting the ratio of the number of matching positions in the twosequences to the total number of positions compared.

The generic term “retinoids” means a group of compounds which includesretinoic acid, vitamin A (retinol) and a series of natural and syntheticderivatives that can exert profound effects on development anddifferentiation in a wide variety of systems. For purposes of thisdisclosure “retinoid” is also intended to encompass an equivalentthereof having the same functional characteristics which may beproduced, for example, by computational chemistry.

“Stringent hybridization conditions” takes on its common meaning to aperson skilled in the art here. Appropriate stringency conditions whichpromote nucleic acid hybridization, for example, 6× sodiumchloride/sodium citrate (SSC) at about 45° C. are known to those skilledin the art. The following examples are found in Current Protocols inMolecular Biology, John Wiley & Sons, NY (1989), 6.3.1-6.3.6: For 50 mlof a first suitable hybridization solution, mix together 24 mlformamide, 12 ml 20×SSC, 0.5 ml 2 M Tris-HCl pH 7.6, 0.5 ml 100×Denhardt's solution, 2.5 ml deionized H₂O, 10 ml 50% dextran sulfate,and 0.5 ml 10% SDS. A second suitable hybridization solution can be 1%crystalline BSA (fraction V), 1 mM EDTA, 0.5 M Na₂HPO₄ pH 7.2, 7% SDS.The salt concentration in the wash step can be selected from a lowstringency of about 2×SSC at 50° C. to a high stringency of about0.2×SSC at 50° C. Both of these wash solutions may contain 0.1% SDS. Inaddition, the temperature in the wash step can be increased from lowstringency conditions at room temperature, about 22° C., to highstringency conditions, at about 65° C. The cited reference gives moredetail, but appropriate wash stringency depends on degree of homologyand length of probe. If homology is 100%, a high temperature (65° C. to75° C.) may be used. If homology is low, lower wash temperatures must beused. However, if the probe is very short (<100 bp), lower temperaturesmust be used even with 100% homology. In general, one starts washing atlow temperatures (37° C. to 40° C.), and raises the temperature by 3-5°C. intervals until background is low enough not to be a major factor inautoradiography.

The invention also includes a method of inhibiting retinoic acidhydroxylation in an organism in need of such inhibition by administeringto the organism an effective amount of an antibody, such antibodiesbeing described herein. A particularly useful antibody for the treatmentof a human would be an antibody to the protein having the amino acidsequence identified as SEQ ID NO:5, or a portion thereof. It would beadvantageous to adapt such an antibody for administration to a human by“humanizing” the antibody, as is understood by those skilled in the art[Hozumi, 1993].

(iv) Kits

Reagents suitable for conducting the above described diagnostic and/ormethods of the invention may be packaged into convenient kits providingthe necessary materials, packaged into suitable containers. Such kitsmay include all the reagents required to detect P450RAI-2 in a sample bymeans of the methods described herein, and optionally suitable supportsuseful in performing the methods of the invention.

In one embodiment of the invention the kit contains a nucleotide probewhich hybridizes with a nucleic acid molecule of the invention, reagentsrequired for hybridization of the nucleotide probe with the nucleic acidmolecule, and directions for its use. In another embodiment of theinvention the kit includes antibodies of the invention and reagentsrequired for binding of the antibody to a P450RAI-2 protein in a sample.In still another embodiment of the invention, the kit includes primerswhich are capable of amplifying a nucleic acid molecule of the inventionor a predetermined oligonucleotide fragment thereof, all the reagentsrequired to produce the amplified nucleic acid molecule or predeterminedfragment thereof in the polymerase chain reaction, and means forassaying the amplified sequences.

The methods and kits of the present invention have many practicalapplications. For example, the methods and kits of the present inventionmay be used to detect P450RAI-2 in any medical sample suspected ofcontaining or lacking P450RAI-2 and used to diagnose diseases associatedwith P450RAI-2 or RA, expression or metabolism or where RA, P450RAI-2inhibitor or P450RAT-2 treatment may be indicated. Examples of suchdiseases include cancer, dysplasia, certain autoimmune diseases ordermatological disorders, angiogenesis, conditions of high order brainfunctions or other conditions as noted herein. Samples which may betested include bodily materials such as blood, urine, serum, tears,saliva, feces, tissues and the like.

Before testing a sample in accordance with the methods described herein,the sample may be concentrated using techniques known in the art, suchas centrifugation and filtration. For hybridization and/or PCR-basedmethods described herein, nucleic acids may be extracted from cellextracts of the test sample using techniques known in the art.

2. Therapeutic Applications

Methods of Treatment/Pharmaceutical Compositions

P450RAI-2 may play a role in a number of diseases, such as thoseassociated with regulation of the cell cycle or apoptosis. In particularP450RAI-2 may play a role in cancer or dysplasia by activatingapoptosis. As such, the invention comprises methods for modulating orsimulating P450RAI-2 activity or P450RAI-2 expression, preferably fortreating or preventing a P450RAI-2 related condition. The inventionfurther comprises uses of the modulating or simulating agents disclosedherein for the preparation of a medicament for treating or preventing acondition associated with P450RAI-2 expression or activity. In anotherembodiment the invention provides a use of the modulating or simulatingagents for the treatment or prevention of a P450RAI-2 related condition.

Accordingly, the present invention provides a method of treating orpreventing a disease associated with P450RAI-2 expression or activitycomprising administering an agent that modulates or simulates P450RAI-2expression or activity to an animal in need thereof, such as in ananimal with cancer, dysplasia an autoimmune disease, or dermatological.

In a preferred embodiment, preferably such agents stimulate or simulateP450RAI-2 activity. Examples of agents that activate or simulateP450RAI-2 activity would include without limitations, P450RAI-2, thegene encoding for P450RAI-2 with suitable promoters, such promoterspreferably being tissue specific promoters and therapeutically effectivefragments of the nucleic acid and amino acid sequences of the invention.

Examples of agents that inhibit P450RAI-2 include antisense nucleic acidmolecules, antibodies and transdominant inhibitors, as described herein.

Agents that inhibit, activate, or stimulate P450RAI-2 can be formulatedinto pharmaceutical compositions with or without RA for administrationto subjects in a biologically compatible form suitable foradministration in vivo. As used herein “biologically compatible formsuitable for administration in vivo” means a form of the substance to beadministered in which therapeutic effects outweigh any toxic effects.The substances may be administered to animals in need thereof. Animals,as used herein refers to any animal susceptible to a disease associatedwith P450RAI-2 expression preferably dogs, cats, mice, horses andhumans.

Administration of an “effective amount” of pharmaceutical compositionsof the present invention is defined as an amount of the pharmaceuticalcomposition, at dosages and for periods of time necessary to achieve thedesired result. For example, a therapeutically active amount of asubstance may vary according to factors such as disease state, age, sex,and weight of the recipient, and the ability of the substance to elicita desired response in the recipient. Dosage regima may be adjusted toprovide an optimum Therapeutic response. For example, several divideddoses may be administered daily or the dose may be proportionallyreduced as indicated by the exigencies of the therapeutic situation.

An active substance may be administered in a convenient manner such asby injection (subcutaneous, intravenous, topical, intratumoral etc.),oral administration, inhalation, transdermal application, or rectaladministration. Depending on the route of administration, the activesubstance may be coated in a material to protect the compound from theaction of enzymes, acids and other natural conditions which mayinactivate the compound.

The compositions described herein can be prepared by known methods forthe preparation of pharmaceutically acceptable compositions which can beadministered to subjects, such that an effective quantity of the activesubstance is combined in a mixture with a pharmaceutically acceptablevehicle. Suitable vehicles are described, for example, in Remington'sPharmaceutical Sciences (Remington's Pharmaceutical Sciences, MackPublishing Company, Easton, Pa., USA 1985). On this basis, thecompositions include, albeit not exclusively, solutions of thesubstances in association with one or more pharmaceutically acceptablevehicles or diluents, and contained in buffered solutions with asuitable pH and iso-osmotic with the physiological fluids.

Recombinant nucleic acid molecules comprising a sense, an antisensesequence or oligonucleotide fragment thereof, may be directly introducedinto cells or tissues in vivo using delivery vehicles known in the artsuch as retroviral vectors, adenoviral vectors and DNA virus vectors.They may also be introduced into cells in vivo using physical techniquesknown in the art such as microinjection and electroporation or chemicalmethods such as coprecipitation and incorporation of DNA into liposomes.Recombinant molecules may also be delivered in the form of an aerosol orby lavage.

The utility of the substances, antibodies, sense and antisense nucleicacid molecules, and compositions of the invention may be confirmed inanimal experimental model systems. Suitable animal model systems whichcan be used to determine P450RAI-2 activity may include, but is notlimited or P450RAI-2 knock-out transgenic animals.

3. Other Applications

Screening for P450RAI-2 Modulating Compounds

In another embodiment, the invention provides a method for identifying acompound or molecule that modulates P450RAI-2 protein activity or geneexpression. “Modulate” as used herein can include activation or increaseof P450RAI-2 protein activity or gene expression or suppression ofP450RAI-2 protein activity or gene expression The method includesincubating components comprising the compound and P450RAI-2 peptide or arecombinant cell expressing P450RAI-2 peptide, under conditionssufficient to allow the components to interact and determining theeffect of the compound on P450RAI-2 activity or expression. The effectof the compound on P450RAI-2 activity can be measured by a number ofassays and may include measurements before and after incubation in thepresence of the compound. Compounds that affect P450RAI-2 activity orgene expression include peptides, chemical compounds and biologicagents. Assays include Northern blot analysis of P450RAI-2 mRNA (forgene expression), Western blot analysis (for protein level) andluciferase, apoptosis or growth suppression assays (for proteinactivity).

The above screening assays may be used for detecting the compounds ormolecules that bind to the P450RAI-2 protein or peptide, in isolatingmolecules that bind to the P450RAI-2 gene, for measuring the amount ofP450RAI-2 in a sample, either peptide or RNA (mRNA), for identifyingmolecules that may act as agonists or antagonists, and the like.

Incubating includes conditions which allow contact between the testcompound and P450RAI-2 peptide or with a recombinant cell expressingP450RAI-2 peptide. Contacting includes in solution and in solid phase,or in a cell. The test compound may optionally be a combinatoriallibrary for screening a plurality of compounds. Compounds identified inthe method of the invention can be further evaluated, detected, cloned,sequenced and the like, either in solution or after binding to a solidsupport by any method usually applied to the detection of a specific DNAsequence such as PCR, oligomer restriction, allele-specificoligonucleotide probe analysis, and the like.

Screening for P450RAI-2 or RA Related Disorders

Method for screening of P450RAI-2 protein activity and or geneexpression as described above, can also be used to screen for P450RAI-2related disorders. For instance, biological samples from patients with aparticular conditions, such as cancer or APL, or other disordersoutlined herein can be screened for P450RAI-2 protein activity and orgene expression. P450RAI-2 gene can also be sequenced from patients witha disorder to identify any mutations in the P450RAI-2 gene. Correlationbetween P450RAI-2 activity and/or gene expression/and or any mutationsand the disorder can be determined by a number of methods known in theart. For instance, P450RAI-2 activity and/or gene expression of asubject to be screened can be compared with that from “healthy”individuals. In one embodiment, the level of P450RAI-2 activity and/orgene expression can be compared with a cut off level for normalP450RAI-2 activity and/or gene expression. In one embodiment, the cutofflevel can be determined by analysis of a database of levels from“healthy” individuals.

Transgenic Animals and Methods of Making Same

Nucleic acids which encode proteins having biological activity ofP450RAI-2 can be used to generate either transgenic animals or “knockout” animals which, in turn, are useful in the development and screeningof therapeutically useful reagents. Preferably, non-human transgenicanimals are encompassed within the scope of this invention. A transgenicanimal (e.g., a mouse) is an animal having cells that contain atransgene, which transgene was introduced into the animal or an ancestorof the animal at a prenatal, e.g., an embryonic stage. A transgene is aDNA which is integrated into the genome of a cell from which atransgenic animal develops. In one embodiment, a P450RAI-2, preferablymouse or human cDNA shown in SEQ ID NO: 4, or an appropriate sequence,can be used to clone a murine P450RAI-2 gene in accordance withestablished techniques and the genomic nucleic acid used to generatetransgenic animals that contain cells which express P450RAI-2 protein.Methods for generating transgenic animals, particularly animals such asmice, have become conventional in the art and are described, forexample, in U.S. Pat. Nos. 4,736,866 and 4,870,009, 5,616,491. In apreferred embodiment, plasmids containing recombinant molecules of theinvention are microinjected into mouse embryos. In particular, theplasmids are microinjected into the male pronuclei of fertilizedone-cell mouse eggs; the injected eggs are transferred topseudo-pregnant foster females; and, the eggs in the foster females areallowed to develop to term. [Hogan, B. et al., (1986) A LaboratoryManual, Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory].Alternatively, an embryonal stem cell line can be transfected with anexpression vector containing nucleic acid encoding a protein havingP450RAI-2 activity and cells containing the nucleic acid can be used toform aggregation chimeras with embryos from a suitable recipient mousestrain. The chimeric embryos can then be implanted into a suitablepseudopregnant female mouse of the appropriate strain and the embryobrought to term. Progeny harbouring the transfected DNA in their germcells can be used to breed uniformly transgenic mice.

Typically, particular cells would be targeted for P450RAI-2 transgeneincorporation by use of tissue specific enhancers operatively linked tothe P450RAI-2-encoding gene. For example, promoters and/or enhancerswhich direct expression of a gene to which they are operatively linkedpreferentially in cardiac muscle cells can be used to create atransgenic animal which expresses a P450RAI-2 protein. Examples ofsuitable promoters and enhancers include those which regulate theexpression of the genes for cardiac myosin and cardiac actin. Transgenicanimals that include a copy of a P450RAI-2 transgene introduced into thegerm line of the animal at an embryonic stage can also be used toexamine the effect of increased P450RAI-2 expression in various tissues.

The pattern and extent of expression of a recombinant molecule of theinvention in a transgenic mouse is facilitated by fusing a reporter geneto the recombinant molecule such that both genes are co-transcribed toform a polycistronic mRNA. The reporter gene can be introduced into therecombinant molecule using conventional methods such as those describedin Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual. ColdSpring Harbor Laboratory press. Efficient expression of both cistrons ofthe polycistronic mRNA encoding the protein of the invention and thereporter protein can be achieved by inclusion of a known internaltranslational initiation sequence such as that present in poliovirusmRNA. The reporter gene should be under the control of the regulatorysequence of the recombinant molecule of the invention and the patternand extent of expression of the gene encoding a protein of the inventioncan accordingly be determined by assaying for the phenotype of thereporter gene. Preferably the reporter gene codes for a phenotype notdisplayed by the host cell and the phenotype can be assayedquantitatively. Examples of suitable reporter genes include lacZ(b-galactosidase), neo (neomycin phosphotransferase), CAT(chloramphenicol acetyltransferase) dhfr (dihydrofolate reductase),aphIV (hygromycin phosphotransferase), lux (luciferase), uidA (bglucuronidase). Preferably, the reporter gene is lacZ which codes forb-galactosidase. b galactosidase can be assayed using the lactoseanalogue X-gal(5-bromo-4-chloro-3-indolyl b-D-galactopyranoside) whichis broken down by b-galactosidase to a product that is blue in color.(See for example Old R. W. & Primrose S. B. Principles of GeneManipulation. An Introduction to Genetic Engineering, 4th ed. OxfordUniversity Press at pages 63-66 for a discussion of procedures forscreening for recombinants).

Additionally, the non-human homologues of genes encoding proteins havingP450RAI-2 activity can be used to construct a P450RAI-2 “knock out”animal which has a defective or altered P450RAI-2 gene. For example, ahuman P450RAI-2 cDNA, comprising the nucleotide sequence shown in SEQ IDNO: 5, or a mouse P450RAI-2 cDNA appropriate sequence thereof, can beused to clone a murine P450RAI-2 gene in accordance with establishedtechniques. A portion of the genomic P450RAI-2 DNA (e.g., an exon) canbe deleted or replaced with another gene, such as a gene encoding aselectable marker which can be used to monitor integration. The alteredP450RAI-2 DNA can then be transfected into an embryonal stem cell line.The altered P450RAI-2 DNA will homologously recombine with theendogenous P450RAI-2 gene in certain cells and clones containing thealtered gene can be selected. Cells containing the altered gene areinjected into a blastocyst of an animal, such as a mouse, to formaggregation chimeras as described for transgenic animals. Chimericembryos are implanted as described above. Transmission of the alteredgene into the germline of a resultant animal can be confirmed usingstandard techniques and the animal can be used to breed animals havingan altered P450RAI-2 gene in every cell. Accordingly, a knockout animalcan be made which cannot express a functional P450RAI-2 protein. Such aknockout animal can be used, for example, to test the effectiveness ofan agent in the absence of a P450RAI-2 protein.

Although experimental animals used in the preferred embodiment disclosedare mice, the invention should not be limited thereto. It can bedesirable to use other species such as rats, hamsters and rabbits.

The transgenic animals of the invention can be used to investigate theeffect of P450RAI-2 expression and activity or lack thereof and to testother compounds and molecules that can perhaps be used to suppress orrestore the P450RAI-2 or RA activity. The transgenic animals of theinvention can also be used to test substances for the ability toprevent, slow or reverse apoptosis. A transgenic animal can be treatedwith the substance in parallel with an untreated control transgenicanimal.

Cells from the transgenic animals of the invention can be cultured usingstandard tissue culture techniques. In particular, cells carrying therecombinant molecule of the invention can be cultured and used to testsubstances for the ability to prevent, slow or reverse apoptosis.

EXAMPLES

General Materials and Methods

Cell Culture

HPK1a-ras (ras-transformed human keratinocyte), COS-1 (African greenmonkey kidney and V79 cells (Chinese Hamster lung) were maintained inDMEM supplemented with 10% FBS (5% for V79). WTE (human non-small celllung carcinoma and SW900 (human non-small cell lung carcinoma) cellswere maintained in RPMI supplemented with 10% FBS. SK-Luci-6 (humannon-small cell lung carcinoma) and SK-MES-1 (human non-small cell lungcarcinoma) cells in RPMI with 5% FBS. NB4(human acute prmyelocyticleukemia-serived) cells were maintained in RPMI supplemented with 10%FBS and gentamicin (10 mg/ml) HeLa cells (human cervical carcinoma) weremaintained in MEM supplemented with 10% FBS. Previous cell lines weresupplemented with penicillin (50 units/ml) streptomycin (50 ug/ml) andfungizone (0.1% final concentration). MCF-7 cells (human breastepithelial adenocarcinoma) were grown in MEM supplemented with 10% FBS,insulin (10 ng/ml), sodium pyruvate (0.5 mM), non-essential amino acids(100 nM), L-glutamine (2 mM), penicillin (5 ug.ml), streptomycin (5ug/ml), fungizone (200 ng/ml), and gentamicin (10 mg/ml). All reagentswere supplied by Life Technologies, NY. Cells lines were maintained at37° C. in an atmosphere of 5% CO₂ and 95% air.

Transient Transfection of Cos-1 Cells

Exponentially growing cells were plated in triplicate into 6-well platesand transfected with lug of pcDNA3.1-P450RAI-1 or pcDNA3.1-P450RAI-2using Fugene 6 transfection reagent with 3 ul per sample as described bythe manufacturer (Roche Molecular Biochemicals, IN). Cells weremaintained in media supplemented with 10% FBS during transfection.

RNA Preparation and Northern Blot Analysis

Total RNA was isolated from cultured cells uding the Oligotex DirectmRNA kit (Qiagen, CA) and electrophoresed on a formaldehyde-agarose gel.Gels were photographed under ultraiolet light and then blotted ontoHybond ECL nitrocellulose membrane (Amersham Pharmacia Biotech, UK) andfixed to the membrane by baking at 80° C. for 2 hours under vacuum.Prehybridization and hybridization steps were performed using ExpressHyb(Clontech, CA) according to the manufacturer's directions. Full lengthP450RAI-1 and P450RAI-2 cDNA were labeled with α-[³²P]dATP usingPrime-A-Gene Labeling System (Promega, Wis.). The blot was washed twotimes for 15 minutes in 2×SSC, 0.1% SDS at room temperature then for 15minutes at 60° C. in 0.1×SSC, and 0.1% SDS and exposed at −70° C. for 19hours to Kodak X-Omat AR film (Eastman Kodak Company, NY).

Example 1 Determination cDNA Sequence Encoding P450RAI-2

The human expressed sequence tagged (EST) database at the NationalCenter for Biotechnology Information (NCBI), available over the Internetat http://www.ncbi.nlm.nih.gov/BLAST/ was searched using an amino acidsequence encoding a typical heme binding motif found in all CytochromeP450s. The database was queried using the following sequence:KKETFIPFGIGKRVCMGEQLAKMELFLMFV (SEQ ID NO1). The TBLASTN algorithm ofthe Advanced BLAST program was used to search all 6 possible readingframes for translation of all the human EST sequences against the querysequence (SEQ ID NO:1). Parameters for all searching were the defaultsof Blosum 62 which use a gap existence cost of 11, per residue cost of 1and lambda ratio of 0.85. Subject amino acid sequences which showedsimilarity to SEQ ID NO:1 were retrieved from the GenBank database andtheir nucleotide sequences used to search GenBank for nucleotidesequences showing similarity to the EST nucleotide query sequence usingthe BLASTN algorithm.

One of the subject sequences obtained from GenBank (AA012833, identifiedhere as SEQ ID NO:2, a 3.5 kb clone from the Soares retina N2b4H2library) showing similarity to the nucleotide sequence encoding aminoacid sequence identified as SEQ ID NO:1, also showed similarity to ahuman genomic DNA sequence from GenBank (Accession#, AC007002 (clonename NH0493L16), identified here as SEQ ID NO:3). As described below,the present inventors determined that this clone comprised within it thepolynucleotide sequence encoding the novel cytochrome P450 of theinvention, P450RAI-2. A BLASTN search of the EST database using SEQ IDNO:2 failed to identify any more EST sequences showing similarity. Inorder to check for protein sequences which may show similarity to the 6possible reading frames for translation of SEQ ID NO:2, the BLASTXprogram was run on the non-redundant GenBank database. Several sequenceswith the highest degrees of amino acid similarity were identified andincluded, human, mouse, Xenopus and zebrafish P450RAI (CYP26A; proteinencoded by SEQ ID NO:13 (human), protein encoded by SEQ ID NO:14(zebrafish)).

Using the amino acid sequence of human P450RAI (SEQ ID NO:4 of WO97/49815) aligned to the 3 possible reading frame translations of SEQ IDNO:3, a potential full-length amino acid sequence for a novel CYP cDNAfamily member was assembled. The intron/exon boundaries were deducedbased on the loss of amino acid similarity. The intron/exon boundariesof the novel cytochrome P450 is shown in FIG. 1. The amino acids withinthe respective exons are identified above the schematic diagram andnucleotide positions in relation to human sequence are provided belowthe diagram. However, it would be appreciated that the positions of theexons noted in FIG. 1 are approximate and may vary slightly from theactual boundaries. The sequence has been termed P450RAI-2 based on itssequence homology with CYP26A. An amino acid sequence comparison betweenhuman P450RAI-2 and human p450RAI-1 is shown in FIG. 3. Overall the twoprotein sequences show 42% identity at the amino acid level and 52% atthe nucleotide level over the region of the predicted open readingframe. The overall similarity of the two putative open reading frames issomewhat higher when conservatively substituted amino acids areconsidered.

Human retina Marathon-Ready cDNA (Clontech, California) was used as atemplate to amplify P450RAI-2 using the polymerase chain reaction (PCR)according to the manufacturer's directions Using the potentialnucleotide sequence derived from the intron/exon mapping exercise, twoprimers, (SEQ ID NO:9 and SEQ ID NO:10) one upstream of the putativeinitial methionine and one downstream of the putative stop codon, weresynthesized and used to PCR amplify a fragment of approximately 1600base pairs representing the coding region SEQ. ID NO: 4 See FIG. 2 [SEQID NO:28] which depicts the original clone within the 1598 bp codingsequence and the 3 untranslated region which was cloned and sequenced.The 1598 bp fragment including the coding sequence of the cDNA isindicated as SEQ ID NO:4 and appears to correspond to a full-lengthcDNA. SEQ ID:4 shows a single nucleotide change from “C” in the genomicsequence SEQ ID NO:3 to “T” at nucleotide 1401 of SEQ ID NO:4 which, dueto the degeneracy of the genetic code, does not change the correspondingamino acid sequence, identified as SEQ ID NO:5.

The cDNA 1600 bp PCR amplified product was gel purified using theQIAEXII Gel Extraction kit (Qiagen, California) and ligated into thepT-Adv vector using T4 DNA Ligase, heat shocked into competent TOP10F′Escherichia coli, plated on Luria Bertoni-kanamycin plates and incubatedovernight at 37° C., as per the manufactures instruction for theAdvanTAge PCR Cloning Kit (Clontech, CA). White colonies were grown upin Luria Bertoni-kanamycin medium, and DNA was prepared using theQIAprep Spin Miniprep kit (Quiagen, CA). For transient expressionstudies the P450RAI-2 cDNA was subcloned into the EcoR1 restrictionendonucleoase site of pcDNA3.1 (Invitrogen, CA).

Example 2 P450RAI-2 Tissue Expression

Given the presence of a full-length cDNA in a retinal cDNA library,expression in human retinal tissues could be expected. In order to findtissues in which P450RAI-2 is expressed, a multi-tissue RNA dot blotcontaining samples from 76 different normal human tissues a human polyA+ blot (Clontech, CA) was probed using a labeled probe encoding thefull length P450RAI-2 α-[³²P]dATP-labeled probe for the correspondingcDNAs were hybridized to blots using the conditions as described in themanufacturers directions. A human brain multi-tissue northern blot(Clontech, CA) was also hybridized with full-length α-[³²P]dATP-labelledP450RAI-2 probe according to the manufacturer's directions. The blotswere stripped and re-probed with α-[³²P]dATP-labelled ubiquitin andβ-actin controls.

FIG. 4 illustrates the results. P450RAI-2 appears to be expressed in avariety of tissues in differing levels (other data not shown) and athigher levels in tissues including kidney, lung, liver, spleen, fetalspleen, skeletal muscle, thymus, peripheral blood leukocyte, lymph node,bone, stomach, placenta, duodenum and pituitary gland. However, samplesfrom human brain including pons (FIG. 4A, sample h1) and left and rightcerebellum (FIG. 4A, samples a2 and b2 respectively) clearly show thehighest levels of expression. FIG. 4C depicts the tissue map of the 76tissue samples. In comparison, a similar blot probed with P450RAI-1shows low level expression in most of the tissues with the absence of adistinct signal in any of the corresponding tissues from human brain(data not shown). Blots shown in FIGS. 4A and 4B are representative ofmultiple hybridization experiments. Two independent blots were utilizedand each blot was hybridized with probes for P450RAI-2, P450RAI-1 andubiquitin control (FIG. 4B in order to verify the results.

A human Northern blot (FIG. 4D)(Clontech, CA) comprising mRNAs fromvarious brain tissues was also probed with P450RAI-2 [SEQ ID NO:4]according to the manufacturers directions. A hybridizing transcript ofgreater than 4.4 Kb was seen and is consistent with the size predictedby the cDNA clone isolated from human retina and from the predictedexons of the genomic clone that was identified. Consistent with the dotblot analyses, considerably higher levels of expression of transcriptsfor P450 RAI-2 are seen in the cerebellum. Lower but detectable levelsof expression are observed in cerebral cortex, medulla, occipital pole,frontal lobe and temporal lobe. Other data from a Northern blotcomprising mRNAs from multiple tissues indicated various levels ofexpression of P450RAI-2 in brain, heart, skeletal muscle, spleen,kidney, liver and small intestine. [Data not shown]

Example 3 Inducibility of P450RAI-2

The regulation of P450RAI-2 expression by various retinoids was checkedin three different human cell lines, SKMES, CALU-1 and MCF-7. See FIGS.5A (P450RAI-2 probe), B (blot was stipped and re-probed with β-actin)and C is ethidium bromide stained gel showing 18S and 28S RNAs. Tissueculture cells were incubated with each retinoid for 12 hours, total RNAprepared and a northern blot performed. The blot was hybridized with SEQID NO:4 using ExpressHyb (Clontech, CA) according to the manufacturer'sdirections at 65° C. The blot was washed as follows: 2×SSPE & 0.1% SDStwo washes of 5 minutes each; 1×SSPE & 0.1% SDS one wash of 15 minutesat 65° C.; 0.1×SSPE & 0.1×SDS one wash of 15 minutes at 65° C. The blotwas exposed to film for 66 hours. P450RAI-2 was found to be induced inMCF-7 cells in response to both all-trans retinoic acid and 13-cisretinoic acid. Whether or not 9-cis retinoic acid induces expression ofP450RAI-2 is not clear from these results. It is known that aliquots ofboth 9-cis and 13-cis retinoic acid are frequently contaminated withall-trans retinoic acid.

P450RAI-2 expression was found to be inducible in the human keratinocytecell line HPK1A-RAS. Cells in culture were incubated with all-transretinoic acid at a final concentration of 10⁻⁶ M for 12 hours. Total RNAwas prepared and a northern blot performed. The blot was hybridized at65° C. using PerfectHyb (Sigma, MO) according to the manufacturer'sdirections. The blot was washed as follows: 2×SSC & 0.1% SDS two washesof 5 minutes each at room temperature; 1×SSC & 0.1% SDS one wash of 15minutes at 65° C.; 0.1×SSC & 0.1% SDS three washes of 15 minutes each at65° C. The blot was exposed to X-ray film overnight. The results areshown in FIG. 6.

The potential induction of mRNAs for P450RAI-2 in response toall-trans-RA was also evaluated.

Tissue culture cells were incubated with 1 μM all-trans-RA dissolved indimethylsufoxide (DMSO) or DMSO alone for 12 hours, total RNA preparedand a northern blot analysis performed. The blot was hybridized at 65°C. using ExpressHyb (Clontech, CA) according to the manufacturersdirections. The blot was washed as follows: 2×SSPE & 0.1% SDS two washesof 5 minutes each; 1×SSPE & 0.1% SDS one wash of 15 minutes at 65° C.;0.1×SSPE & 0.1×SDS one wash of 15 minutes at 65° C. The blot was exposedto X-ray file for 66 hours.

RT-PCR was performed using 1 μg total RNA and the Advantage One-StepRT-PCR kit (Clontech, CA). The final primer concentrations were 45 μMfor the P450RAI-2 primers and 11.25 μM for the GAPDH-specific primers.The thermal cycling program for cDNA synthesis and PCR amplification was1 cycle at 50° C. for 1 hr, 1 cycle at 94° C. for 5 min, followed by 30cycles of 94° C. for 30 sec, 65° C. for 30 sec, 68° C. for 1 min, and afinal cycle for 68° C. for 2 min. The P450RAI-2 upstream amplificationprimer was 5′-TCCCTGCCTGTCGACCTGCCCTTC-3′ (SEQ ID NO: 29) and thedownstream primer was 5′-GACACTCCAGCCTTTGGGGATCTG-3′ (SEQ ID NO: 30).The upstream and downstream primers to detect humanglyceraldehyde-3-phsophate dehydrogenase mRNA were respectively,5′-TGAAGGTCGGAGTCAACGGATTTGGT-3′ (SEQ ID NO:31) and5′-CATGTGGGCCATGAGGTCCACCAC-3′ (SEQ ID NO:32).

The RT-PCR products were electrophoresed on a 1.2% agarose gel andblotted onto Hybond-N⁺ membrane (Amersham Pharmacia Biotech, UK).Hybridization was performed at 42° C. using ExpressHyb hybridizationbuffer (Clontech Laboratories Inc., CA) and probed with an internalP450RAI-2-specific oligonucleotide,5′-GTGTGCCCTCGCAGGGGCAGCCGCCACTGTGC-3′ (SEQ ID NO: 33) that had beenend-labeled using γ[³²P]ATP and T4 polynucleotide kinase. The membranewas subsequently stripped and re-probed with an internal-end labeledP450RAI-1-specific oligonucleotide,5′-CGCCTCGGATGCCCGCAGCCC-GCAGATCTTGG-3′ (SEQ ID NO: 34) The membrane wasagain stripped and re-probed with an internal GAPDH oligonucleotide. Thefinal wash for all hydbridizations was 0.1×SSC/0.1%, 50° C., 15 min,blots were exposed to Kodak X-0mat AR film (Eastman Kodak Co., NY).

Several human cell lines in culture were tested for expression andinduction of expression of P450RAI-2 by treating cells with 1 μMall-trans-RA or DMSO for 12 hours followed by Northern blot and RT-PCRanalyses (FIG. 7A). Of the four cell lines tested by Northern analysis,three (HPK1a-ras, HeLa and MCF-7) show induction of P450RAI-2transcripts in response to all-trans-RA with MCF-7 showing the strongestinduction.

Reverse transcription polymerase chain reaction (RT-PCR) analyses oftranscripts from both control and all-trans-RA treated cultured cellsdemonstrate several important findings. As with P450RAI-1, P450RAI-2shows multiple distinct modes of regulation of expression (FIG. 7B).NB4, V79, and SK-Luci-6 cells appear to have little or no perceptibletranscripts for P450RAI-2 in either vehicle or all-trans-RA treatedcells. Several cell lines, including MCF-7, HeLa, HPK1a-ras and WT-Eshow evidence for inducible expression of P450RAI-2 when cells areexposed to 1 μM all-trans-RA. Interestingly, SKMES-1 and SW900, showsconstitutive expression of P450RAI-2 in both treated and untreatedsamples.

Using RT-PCR we also evaluated a brief time course of induction of PCRproducts corresponding to mRNA transcripts for P450RAI-2 in HPK1a-rascells. These results (FIG. 7C) indicate that, at least in one cell line,transcripts for P450RAI-2 can be induced by all-trans-RA within 2 hourspost-addition of inducer suggesting a direct transcriptional mechanismof induced.

Example 4 P450RAI-2 Homologs

The existence of homologs of P450RAI-2 in other species was explored.SEQ ID NO:4 and the BLASTN algorithm was used in a search of the NCBIEST database. Initially, three homologs were identified, one each frommouse, rat and zebrafish. The nucleotide sequences of these clones, SEQID NO:6, (mouse) SEQ ID NO:7 (rat) and SEQ ID NO:8 (zebrafish) showextensive similarity to SEQ ID NO:5. The corresponding amino acidsequences of the mouse and zebrafish are given as SEQ ID NOs:11 and 12,respectively.

The clones for mouse, zebrafish and rat are all partial cDNAs andencoding portions corresponding to portions of the full-length codingsequence of the human cDNA (SEQ ID NO:4). The zebrafish amino acidsequence, which shows homology to P450RAI-2, contains 167 amino acidresidues. Of the 167 amino acids, 115 are identical to the human CYP26Asequence (i.e., when the amino acids are aligned using the Omigasoftware program (Oxford Molecular, Campbell, Calif.), version 1.13,with the default parameter settings for protein alignments, 115 are thesame), giving a homology of about 68 percent. The rat sequence showsnucleotide homology to the 3′-untranslated region of human P450RAI-2 sono conclusion about the degree of homology to the coding region ofP450RAI-2 can be made. The mouse amino acid sequence shows an absoluteconservation with the human counterpart. Over a stretch of 92 aminoacids beginning with the potential start methionine of the humanP450RAI-2, all 92 amino acids are conserved between the mouse and human.At the nucleotide level there is 93.1 percent homology between the mouseand human. This degree of homology is exceptionally high, but this is apreliminary result in the sense that the full-length mouse sequenceshave yet to be obtained. The open reading frame of the mouse nucleotidesequence extends at least 111 amino acids upstream of the putativeinitial methionine in human P450RAI-2, raising a possible question as tothe true origin of the mouse sequence.

Further searching of the NCBI Mouse EST database available over theinternet at http://www.ncbi.nlm.nih.gov/blast/blast.cgi?[form=1] usingthe human P450RAI-2 sequence revealed three mouse EST clones, AW488377.1(SEQ ID NO:18) which corresponds to human cDNA nucleotides 271-831,AW047279.1 (SEQ. ID. NO:19) which corresponds to human cDNA nucleotides1-276 and includes 5′ UTR ATG is underlined in bold, wherein thesequence should be read backwards in antisense from this point, and ESTBE864840.1 (SEQ. ID. NO:20) which corresponds to human cDNA nucleotides1-118 and includes 5′UTR; ATG is marked. In sequencing clone AW488377,the inventors identified a novel sequence included therein, SEQ ID NO:26. A further rat EST, SEQ ID NO: 27 was also identified thatcorresponds to human P450RAI-2 nucleotides 1-388.

The ESTs were used to search the HTGS database http://www.ncbi.nlm.nih.gov/blast/blast.cgi.?[form=1] wherein genomic mouse cloneAC022779.3 was identified, potentially comprising the complete mousenucleotide coding sequence of P450RAI-2. Using techniques similar tothat used to identify the intro/exon boundaries of human P450RAI-2, themouse clone was aligned with the human P450RAI-2 cDNA to detectsimilarities. Five of Six putative mouse exon sequences were identified:SEQ ID NO: 21 (corresponds to exon 1, mouse sequence 185832-186036), SEQID NO: 22 (corresponds to exon2, mouse sequence 189360-186590), SEQ IDNO: 23 (corresponds to exon 3, mouse sequence 196630-196905, SEQ ID NO:24 (corresponds to exon 4, mouse sequence 197146-197303), and SEQ ID NO:25 (corresponds to exon 6, mouse sequence 90745-90366).

Example 5 Metabolism of All-trans Retinoic Acid by P450RAI-2

Analysis of All-trans-RA Metabolism by HPLC.

48 hours post-transfection, cells were washed twice with DMEM medium(without serum) and then incubated in 0.5 ml DMEM medium containing 10%FBS and either 100 nM radiolabelled all-trans-RA (0.1 μCi/ml[³H]-RA;5nCi/nmol) or unlabelled 1 μM all-trans-RA. After incubation for 3 hoursat 37° C., in a light protected environment, total lipids were extractedas described previously by Bligh and Dyer [1957] as modified in Whiteand Petkovich [1996b]. The aqueous soluble retinoid metabolites werequantified using β-scintillation counting. The organic solublemetabolites were dried under nitrogen gas, resuspended in 100 μlacetonitrile:water:acetic acid in the ratio 50:50:0.5 and analyzed byHPLC. HLPC was performed using a reverse phase column (150×4.6 mm C18Zorbax-SB, Hewlett Packard) at a flow rate of 1 ml/min. The Mobile phasecontained 10 mM ammonium acetate and consisted of an isocratic elutionfor 2 min with solvent A (acetonitrile; water:acetic acid 50:50:0.5)followed by a linear gradient over 18 min from solvent A to solvent B(acetonitrile:water:acetic acid 90:10:0.04) and then an isocraticelution with solvent B for an addition 5 min. Effluent from the HPLCcolumn flowed directly to a radioflow detector LB (EG&G Berthold). Theretinoids were detected at a wavelength of 351 nm and the ultravioletspectrum of each metabolite peak was determined using photodiode arraydetection. Radioactivity as well as ultraviolet spectrum data wasanalyzed using Millenium 32 software (Waters, Mass.). Aqueous solubleradioactivity (FIGS. 14A and B) was calculated by integration ofselected regions of the chromatograms. Three regions of thechromatograms were defined which represent: (I) the substrate peak(all-trans-RA); (ii) peaks with retention times between 8 and 12 minutes(4-OH region); and more polar peaks with retention times between 2 and 6minutes (polar region).

Example 5A

Retinoic acid as a substrate of P450RAI-2 was studied. The full-lengthhuman P450RAI-2 cDNA was cloned into the eukaryotic expression vectorpcDNA 3.1 (Invitrogen, CA). Exponentially growing COS-1 cells wereplated in triplicate into 6 well plates and transiently transfected with1 ug of pcDNA 3.1, pcDNA3.1-P450RAI-1, or pcDNA3.1-P450RAI-2 usingFugene 6 transfection reagent with 3 ul per sample as described by themanufacturer (Roche Molecular Biochemicals, IN) and then incubated withnanomolar concentrations of [11,12−³H]all-trans retinoic acid ormicromolar concentrations of non-radioactive all-trans retinoic acid.COS-1 cells are an African green monkey kidney “fibroblast-like” cellline. The cell line was maintained in DMEM supplemented with 10% FBS at37° C. in an atmosphere of 5% CO₂ and 95% air.

P450RAI-2 expression in COS-1 cells promoted the rapid conversion of RAinto both lipid- and aqueous-soluble metabolites. See FIGS. 8 to 13.Fractions of total lipid extracts of transfected cells were initiallyseparated by reverse-phase HPLC on Zorbax-SB C18 column (HewlettPackard). HPLC conditions used a linear gradient of 50% acetonitrile,49.9% H₂O, 0.1% acetic acid to 90% acetonitrile, 9.9% H₂O, 0.1% aceticacid with a flow rate of 1 ml/minute. Radioactivity was detected using aBerthold RadioFlow monitor. Using these conditions standard retinoidseluted at the following times: all-trans retinoic acid—20.5 minutes;4-OH-retinoic acid—8.1 minutes; 4-oxo-retinoic acid—9.6 minutes; and18-OH-retinoic acid—9.9 minutes. Comparison between extracts from pcDNA3.1 and pcDNA 3.1-P450RAI-2 cells indicated that P450RAI-2 significantlyincreased all-trans retinoic acid metabolism. Incubation of P450RAI-2transfected cells with micromolar concentrations of all-trans retinoicacid resulted in the production of multiple more polar peaks, some ofwhich co-eluted with the standard retinoids. FIG. 8A shows an increasein aqueous-soluble radioactivity in P450RAI-2 transfected cells comparedto media or pcDNA alone. FIG. 8B shows that there was an increase inlipid-soluble metabolites of all-trans retinoic acid when P450RAI-2 wastransfected into the COS-1 cells. Metabolism of micromolarconcentrations of non-radioactive all-trans retinoic acid was alsoevaluated. Transfected cells and controls were exposed to 1 micromolarall-trans retinoic acid for 3 to 4 hours and then analyzed formetabolism. Photo-diode array detection of HPLC-separated peaks areshown in FIGS. 10 to 13. FIG. 10 shows a background profile of mediaalone. FIG. 12 shows COS-1 cells transfected with the pcDNA plasmidalone. FIG. 12 shows the generation of more polar products when P450RAI(human) is transfected. In comparison, in FIG. 13, P450RAI-2 also causesthe rapid metabolism of all-trans retinoic acid substrate to polarmetabolites, several of which have the same retention times as theretinoid standards for 4-OH-retinoic acid and 4-oxo-retinoic acid.Although similar, there appear to be some differences in the ratios ofindividual metabolites in the profiles generated by P450RAI-2 comparedto P450RAI.

Example 5B

COS-1 cells were transfected with either plasmid (pcDNA3.1-P450RAI-2 orpcDNA3.1-P450RAI-1). The cells were then incubated with, all-trans-RAsubstrate over a 3 hour incubation period. The all-trans-RA substratewas extensively metabolized to more polar aqueous soluble products(FIGS. 14 and 15). HPLC analysis using photodiode array detection wasperformed on samples prepared from transfected cells trated with 1 μMunlabelled all-trans-RA. FIGS. 14A, B and C show comparativechromatograms of the lipid-soluble extracts from pcDNA3.1-P450RAI-2(FIG. 14A), pcDNA3.1-P450RAI-1 (FIG. 14B) and pcDNA3.1 transfected cells(FIG. 14C). In both pDNA3.1-P450RAI-2 and pcDNA3.1-P450RAI-1 transfectedcells the generation of multiple more polar peaks is observed. There isalso a significant decrease in all-trans-RA substrate when compared topcDNA3.1 controls (compare RA peaks in FIGS. 14A, B, with C). Peakslabelled as 4-OH-retinoic acid, 4-oxo retinoic acid and 18-OH-retinoicand co-elute with standards of and show characteristics UV spectra ofthese metabolites. Additionally, multiple unidentified peaks (labeled1-4; FIG. 14A) which show maxima characteristic of retinoids (data notshown) are generated and appear to be qualitatively similar in bothP450RAI-2 and P450RAI-1 samples compared to controls.

To evaluate the efficiency of P450RAI-2 at more physiologicalconcentration of substrate, P450RAI-1 transfected cells were exposed to100 mM radiolabelled (spec. act.) all-trans-retinoic acid (FIGS. 15A andB). In these cells, 34±0.2% of the all-trans-RA substrate is convertedto aqueous-soluble products compared to 26±1.5% in the P450RAI-1transfected cells (FIG. 15A). Controls, including media alone orpcDNA3.1 tranfected cells, show 1.6±0.1% (media alone) and 2.7±0.2%(pcDNA3.1) conversion of substrate to aqueous radioactivity.

The radioactivity remaining in the organic soluble fraction in thetransfected cells exposed to 100 nM [³H] all-trans-retinoic acid (FIG.15B) was also evaluated. HPLC analysis identified many more polarmetabolites in both the P450RAI-2 and P450RAI-1 transfected cellscompared to controls (data not shown). In media from cells transfectedwith pcDNA3.1-P450RAI-2 or pcDNA3.1-P450RAI-1 a high degree ofdisappearance of substrate compared to controls was observed. As well,there is a concomitant increase in the more polar lipid-soluableretinoid metabolites which elute in both the 4-OH and polar regions ofthe chromatograms. These results clearly indicate that expression ofeither P450RAI-2 or P450RAI-1 causes substantial metabolism ofall-trans-RA to more polar metabolites (FIG. 15B).

Example 6 Retinoid Substrate Specificity of P450RAI-2

Given the presence of two unique enzymes P450RAI-1 and P450RAI-2, withthe capacity to rapidly metabolize all-trans-RA the specificity of thesetwo enzymes were evaluated. Interestingly, both P450RAI-1 and P450RAI-2show approximately equal efficiencies at metabolizing all-trans-RA(FIGS. 15 and 16). Competition assays were also performed to evaluatethe ability of five retinoids, all-trans-RA, 9-cis-RA, 13-cis-RA,retinal and retinol to compete out P450RAI-2 or P450RAI-1 mediatedall-trans-RA metabolism (FIG. 16). The non-specific cytochrome P450inhibitor, ketoconazole, was also tested.

COS-1 cells were transfected with either pcDNA3.1-P450RAI-1 orpcDNA3.1-P450RAI-2 in 6-well tissue culture plates as described above.48 hours post-transfection cells were harvested, pooled, washed withDMEM medium and replated into duplicate 48-well plates with 5×10⁵ cellsper well. The cells were incubated in 0.2 ml DMEM medium containing 0.05μCi/ml [³H]-RA (final concentration 2 nM) in the present or absence ofincreasing concentrations of the each unlabelled retinoids(all-trans-RA, 9-cis-RA, 13-cis-RA, retinol, retinal). Control cellswere incubated with increasing concentration of ketoconazole. Afterincubation for 3 hours at 37° C., the retinoids were extracted using theBligh and Dyer [1957] procedure and the aqueous soluable RA-metaboliteswere counted in a scintillation counter as described above.

These competition studies indicated that P450RAI-1 and, -2 exhibitcomparable substrate specificies with all-trans-RA being the preferredsubstrate for both enzymes having ID₅₀ values of approximately 3.0 μMfor P450RAI-2 and 2.5 μM for P450RAI-1. The other retinoids show varyingabilities to compete out metabolism of all-trans-RA by P450RAI-2 andP450RAI-1 in the following rank order:9-cis-RA>13-cis-RA>retinal≧retinol (see Table 1 for interpolated ID₅₀values). Using microsomes prepared from stably-transfected P450RAI-1cells we have also found the same relative levels of competitionsuggesting that the differences in ID₅₀ values are not due differencesin cellular uptake of the retinoids (data not shown).

TABLE 1 INTERPOLATED ID₅₀ VALUES P450RAI-1 P450RAI-2 All-trans-RA 2.5 39-cis-RA 32 25 13-cis-RA >75 55 Retinol >100 >100 Retinol >100 >100Ketoconzole 16 12

Example 7 Expression of P450RAI-1 and P450RAI-2 in Human Cells

Total RNA aliquots (10 μg) were electrophoresed on a 1.0%formaldehyde-agarose gel and a northern blot performed. The gel wasphotographed under ultraviolet light and then blotted on Hybond ECLnitrocellulose membrane (Amersham Pharmacia Biotech, UK) and fixed tothe membrane by baking at 80° C. for 2 hours under vacuum.Prehybridization and hybridization steps were performed using ExpressHyb(Clontech, CA) according to the manufacturer's directions. Threeindividual cDNA fragments were labeled with α-[³²P]dATP using thePrime-A-Gene Labeling System (Promega, WI). The probes were as follows;P450RAI-1762-1217 bp of SEQ ID NO:13, full length P450RAI-2 SEQ ID NO:4and a human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) PCRfragment. The blot was hybidized with P450RAI-2, washed two times for 5minutes in 2×SSPE, 0.1% SDS at room temperature, then washed once at 65°C. for 10 minutes in 1×SSPE, 0.1% SDS and a final wash for 15 minutes at65° C. in 0.1×SSPE, 0.1% SDS. The blot was exposed at −70° C. for 48hours to Kodak X-Omat AR film (Eastman Kodak Company, NY). FIG. 17Ashows P450RAI-2 expression was induced in the RAFT sample treated withTazarotene. P450RAI-2 appears to also be expressed in the Day14Psoriasis Biopsy sample treated with Tazarotene. The blot was strippedby washing two times for 30 minutes in boiling 0.5% SDS and exposed tofilm overnight to ensure proper removal of probe. The above protocol wasrepeated for P450RAI-1 and GAPDH. The P450RAI-1 and GAPDH blots wereexposed for 96 and 4 hours respectively. Two separate hybridizationswith a P450RAI-1 probe did not produce any bands on the northern blot.

RT-PCR was performed using lug of total RNA and the Advantage One-StepRT-PCR kit (Clontech, CA). The final primer concentrations were 45 μMfor the P450RAI-1 and P450RAI-2 primers and 11.25 μM for theGAPDH-specific primers. Two separate sets of reactions were performedusing the primer sets, P450RAI-1/GAPDH and P450RAI-2/GAPDH. The thermalcycling program for cDNA synthesis and PCR amplification was 1 cycle at50° C. for 1 hour, 1 cycle at 94° C. for 5 minutes, followed by 30cycles of 94° C. for 30 seconds, 65° C. for 30 seconds, 68° C. for 1minute and a final cycle of 68° C. for 2 minutes. The P450RAI-1,P450RAI-2 and GAPDH upstream and downstream amplification primers setswere 5′GCCTTCGAGGAAATGACCCG-3′ (SEQ ID NO: 35) and5′-CTGGATGCATCCTCTGGGTG-3′ (SEQ ID NO: 36), 5′-GTCTACCAGCAGTTTGTGGAC-3′(SEQ ID NO: 37) and 5′-AGTCCAGGTAGCGCAGCCCACT-3′ (SEQ ID NO: 38),5′-TGAAGGTCGGAGTCAACGGATTTGGT-3′ (SEQ ID NO: 39) and5′-CATGTGGGCCATGAGGTCCACCAC-3′ (SEQ ID NO: 40) respectively. Total RNAisolated from MCF-7 cells treated with all-trans-RA was used as apositive control. FIG. 17B also shows expression of P450RAI-2 in theTazarotene treated RAFT sample. Both the Psoriasis samples show PCRproducts corresponding to P450RAI-2.

Example 8 Expression of P450RAI-2 in Mouse Embryos

Probe synthesis: All in situ hybridization experiments were performedusing an antisense copy of mouse EST AW488377.1 [SEQ ID NO:18] labelledwith digoxigenin. The EST was cloned into pT7T3D, linearized withHindIII, and transcription was initiated from the T7 promoter. RNAlabeling reactions were performed using DIG RNA labeling mix (Roche) asper instructed by the kit insert.

In Situ Hybridization: Mice were sacrificed by cervical dislocation, andembryos were dissected in 1×PBS, before being left to fix overnight in4% paraformaldehyde at 4° C. The next day, embryos were washed twicewith PBT (1×PBS, 0.1% Tween-20) for 5 minutes at 4° C. Embryos werewashed 5 minutes each with 25, 50, 75% methanol in PBT, then twice with100% methanol and then stored at −20° C. To rehydrate embryos, they weretaken through the previous methanol series in reverse and washed twicewith PBT. Then embryos were treated with 10 μg/mL proteinase K in PBTfor the following times: 8.5 dpc (days post coitum)-no treatment; 9.5dpc-3 minutes; 10.5 dpc-4 minutes; 11.5 dpc-5 minutes. 3 washes of 2mg/mL glycine in PBT were performed for 5 minutes each. Embryos wererefixed in 0.2% glutaraldehyde/4% paraformaldehyde in PBT for 20minutes, and then washed twice with PBT for 5 min. 1 mL ofprehybridization solution (5×SSC, 1% SDS, 5 μg/mL Yeast tRNA, μg/mLheparin) was added, and embryos were incubated at 70° C. After 1 hour,prehybridization solution was replaced with 1 mL of fresh solutioncontaining 1 μg digoxigenin-labeled probe and left to hybridizeovernight at 70° C. The next day, embryos were washed twice withprehybridization solution for 30 minutes at 70° C. Embryos were washedfor 20 minutes at 70° C. with a 1:1 mix of prehybridization solution and1×MABT (DIG Wash and Block Buffer Set, Roche). After 3 rinses with MABT,embryos were washed twice for 30 minutes at 70° C. with MABT. Topreblock embryos, 1×MABT/2% Blocking Reagent (DIG Wash and Block BufferSet, Roche) was added. After an hour, solution was removed and replacedwith 1×MABT/2% Blocking Reagent/20% sheep serum and left for 1 hour.Next, 1×MABT/2% Blocking Reagent/20% sheep serum/0.0005 Anti-DigoxigeninAntibody coupled to Alkaline Phosphatase (Roche) was added at leftovernight at 4° C. The next day, embryos were rinsed 3 times with 1×MABTwith 2 mM levamisole, and washed five times for 1 hour in 1×MABT/2 mMlevamisole. Two washes of 10 minutes each were performed in NTMT (100 mMNaCl, 100 mM Tris-HCl, pH=9.5, 50 mM MgCl₂, 2 mM levamisole). 1 mL offresh NTMT was added along with 3.5 μL BCIP and 4.5 μL NBT (Gibco), andcolour reaction was allowed to proceed in the dark. When complete,embryos were rinse twice with PBT, and refixed overnight at 4° C. in0.2% glutaraldehyde/4% paraformaldehyde. The next day, embryos werewashed for 1 hour in 1:1 CMFeT:glycerol before transfer to 4:1CMFeT:glycerol until ready to photograph.

FIG. 18 illustrates P450RAI-2 in 8.0 and 8.5 dpc mouse embryos. (A) 8.0dpc lateral view. No apparent staining. (B) 8.0 dpc, dorsal view.Staining at anterior end of neutral folds. (C) 8.5 dpc, lateral view.Expression is evident, possibly in presumptive rhombmeres 2, 5, and 6.(D) 8.5 dpc, dorsal view, rhombomere expression of RAI2 is clearlyevident. TL: Tail; YS Yolk Sac; NF: Folds; pr: Presumptive Rhombomeres.

FIG. 19 illustrates P450RAI2 in 9.0 and 10.5 dpc mouse embyros. (A) 9.0dpc, lateral view. Specific staining is visible in the eye, andrhombomeres 5 and 6. Diffuse staining is visible where the hind bud isbeginning to form. (B) 9.0 dpc, dorsal view. Rhombomeres 5 and 6 showRAI2 expression. (C) 10.5 dpc, lateral view. The otic vesicle and eyeare stained. (D) 10.5 dpc, dorsal view. Specific staining is observed inboth otic vesicles as well as the hind limb bud. HL: hind limb bud; OV:Otic Vesicle.

FIG. 20 illustrates P450RAI2 staining in 11.5 dpc mouse embryo (A) 11.5dpc, laterial view, staining is visible in both the fore and hindlimbbud. (B) 11.5 dpc, ventral view. Expression of P450RAI2 in both limbbuds (C) Close up of forelimb bud, showing a lack of expression in theapical ectodermal ridge FL: Forelimb bud; HL: Hindlimb bud; AR: ApicalEctodermal Ridge.

FIG. 21 illustrates P450RAI-2 Staining in Embryos Treated with RetinoicAcid (A) 8.5 dpc, lateral view, staining is observed in rhombomere 5 andthe tail mesoderm as indicated by the arrow. (B) 8.5 dpc, dorsal viewclearly showing P450RAI2 expression in rhombomere 5. (C) 9.5 dpc,lateral view, expression of P450RAI2 is observed in rhombomeres 5 and 6,the developing hindlinb, somites and posterior mesoderm. (D) 9.5 dpc,dorsal view, expression is evident in rhombomeres 3,5 and 6 and in trunkectoderm as indicated by the arrow. r: rhombomere; HL; Limb bud.

FIG. 22 illustrates P450RAI-2 expression in 11.5 dpc embryos treatedwith retinoic acid. (A) 11.5 dpc, lateral view, P450RAI2 expression isobserved in both the developing hind and fore limb. (B) 11.5 dpc,ventral view, as in embryos untreated with retinoic acid, P450RAI2expression is not observed in the aptical ectodermal ridge.

Example 9 Assays Using Cell Lines Expressing Different P450RAI's

P450RAI-1 and -2 expression plasmids can be used to generate transfectedcells. Plasmid vectors such as pcDNA3.1 (Invitrogen, CA) are used toexpress cDNA of interest in the cells. Cells such as COS-1 or Hela couldbe used as the host for this purpose. Cells are then exposed to eitherlow concentrations (picomolar) of a radioactive agent (substrate) orhigher concentrations (micromolar) of non-radioactive agent (substrate)and the metabolic profile determined (see Example 5 and internationalpatent publication No. WO 97/49815 in which all-trans retinoic acid is asubstrate but other retinoid or retinoid type compounds can be used).The time of incubation of the cells can vary from 1 hour to 24 or 48hours depending on the amount of agent and levels of expression of theprotein of interest. The representative metabolite profiles aredetermined using phase extraction and HPLC. In the case of radioactivesubstrate β-scintillation counting can also be used if the metabolitesproduced segregate preferentially into one phase, as in the case ofP450RAI-1 and RAI-2 when looking at all-trans retinoic acid metabolism.In comparative testing of potential modulators of P450RAI-1 orP405RAI-2, the modulators could be added to the cells at the same timeas the substrate. Specificity of the modulator is determined byexamining the degree to which its addition affects either thedisappearance of substrate or the production of metabolites.

Example 10 Preparation of Antibodies

Monoclonal antibodies (Mab's) specific for P450RAI-2 are useful, forexample, for diagnostic purposes such as for determining P450RAI-2protein levels in the identification of normal and tumor tissues whichmetabolize RA. To produce these antibodies, purified P450RAI-2 proteinis prepared. The human P450RAI-2 protein is produced in bacterial cellsas a fusion protein with glutathione-S-transferase using the vectorpGEX2 (Pharmacia). This permits purification of the fusion protein byGSH affinity chromatography. In another approach, P450RAI-2 is expressedas a fusion protein with the bacterial maltose binding domain. Thefusion protein is thus recovered from bacterial extracts by passing theextract over an amylose resin column followed by elution of the fusionprotein with maltose. For this fusion construct, the vector pMalC2,commercially available from New England Biolabs, is used. This vectorhas been used in the past, for example, to overexpress nuclear receptorproteins which were recovered in high yields for functional studies andthe production of receptor specific antisera [Ohno, 1993]. Thepreparation of a second fusion protein is also useful in the preliminaryscreening of MAb's.

The generation of hybridomas expressing monoclonal antibodiesrecognizing P450RAI-2 protein is carried out as follows: BALB/c mice areinjected intraperitoneally with protein/adjuvant three times atone-month intervals, followed by a final injection into the tail veinshortly prior to cell fusion. Spleen cells are harvested and fused withNS-1 myeloma cells (American Type Culture Collection, Rockville, Md.)using polyethylene glycol 4000 according to standard protocols [Kennett,1979; Mirski, 1989]. The cell fusion process is carried out as describedin more detail below.

The fused cells are plated into 96-well plates with peritoneal exudatecells and irradiated spleen cells from BALB/Ccmice as feeder layers andselection with hypoxanthine, aminopterin, and thymidine (HAT medium) isperformed.

An ELISA assay is used as an initial screening procedure. 1-10 μg ofpurified P450RAI-2 (cleaved from the fusion protein) in PBS is used tocoat individual wells, and 50-100 μl per well of hybridoma supernatantsis incubated. Horseradish peroxidase-conjugated anti-mouse antibodiesare used for the colorimetric assay.

As a secondary screening, cells which exhibit no detectable expressionof P450RAI-2 message and no detectable RA metabolizing activity in theabsence of retinoic acid, but in which P450RAI-2 exposure to RA inducesexpression of P450RAI-2, are used.

Positive hybridomas are cloned by limiting-dilution and grown tolarge-scale for freezing and antibody production. Various positivehybridomas are selected for usefulness in western blotting andimmunohistochemistry, as well as for cross reactivity with P450RAI-2proteins from different species.

The selected MAb's are useful for monitoring the levels of expression ofP450RAI-2 protein following RA treatment in cell culture and in tissues.P450RAI-2 protein expression may be a prognostic indicator fordetermining whether a particular tumor will respond to RA treatment.There is also a wide intersubject variability in baseline RA metabolismand there is evidence suggesting that subjects with a high rate of RAmetabolism have a higher incidence of squamous or large cell cancers ofthe lung [Rigas, 1996]. Once useful antibodies are characterized, theseantibodies are used to survey tumor tissue samples for P450RAI-2expression.

Protocol for Production of Mouse Hybridomas

Fusion

Feeder cells (spleen and peritoneal exudate cells) are plated. 24 to 48hours before fusion, mouse myeloma cells are taken off drug(8-azaguanine 20 μg/ml) and counted to ensure that there are at least50×10⁶ cells. 2 g of PEG 4000 are autoclaved in a glass tube for 15minutes and maintained at 60° C. for use or alternatively stored at roomtemperature and remelted in a 60° C. water bath when needed.

BALB/c mice are immunized as per desired schedule. The final injectionis given intravenously in the tail vein. Fusion of immunized spleencells is carried out 3 or 4 days after the intravenous injection. Spleenfrom each animal is collected separately; eye sera for ELISA if desired.

A single cell suspension is prepared using a Teflon pestle and decantingconnective tissue. The suspension is washed 1× in serum-free medium.Each spleen has about 10×10⁶ cells. The myeloma cells are collected,counted and washed in serum-free medium.

The cells are then fused. A small beaker of water, and serum-free medium(37° C.) are prepared and the PEG melted at 50-60° C. The immunizedspleen cells and myeloma cells are mixed in a 50 ml TC tube (recommendedratios vary from 1:1 to 2:1) and the cells are washed once withserum-free medium. The supernatant is carefully discarded. 2.4 mlpre-warmed serum-free medium is added immediately with pipette to themelted PEG and mixed, maintaining the temperature at 37° C. in beaker ofwarm water. The PEG should be light pink. If it is yellow, anotheraliquot should be used. 0.5-1.0 ml of PEG is added dropwise to the cellpellet over 1 minute with gentle rotation of the tube or gentle stirringto ensure mixing. The tip of the addition pipette is placed directlyover the cell pellet. The tube is swirled gently in 37° C. water bathfor 90 seconds with the blunt end of a 3 ml pipette tip and 10 ml warmserum-free medium added slowly over 6-10 minutes while rotating tubegently to bring the volume up to 20-50 ml. The tube is maintained at 37°C. for at least 20 minutes to obtain cell fusion and then the cells arewashed 2× with serum-free medium. The cells are centrifuged and gentlyresuspended in 100 ml of pre-warmed medium +10-20% FBS. 100 μl/wellaliquotted in 96-well plates. Assuming one spleen fused with 100×10⁶cells myeloma fusion partner, about 10 plates are needed. On thefollowing day, 100 μl medium is removed and 100 μl 2×HAT added. Feedwith 1×HAT medium for 1 to 3 weeks, then feed with HT medium (i.e.,remove ½ HAT medium and replace with equal volume HT medium).

Preparation of Peritoneal Exudates and Spleen Feeder Cells

A sacrificed mouse is sprayed with 70% alcohol, skin is nicked and tornapart, with care being taken not to cut the peritoneum. The peritoneumis lifted with forceps and a needle is introduced; 5 ml of serum-freemedium is slowly injected. The abdomen is massaged and the fluid isslowly sucked up, collected in a sterile tube and kept on ice. Thevolume is brought up to 5 ml. The spleen is obtained and placed in asterile tube containing serum-free medium. The spleen is gently mashedwith a sterile Teflon pestle. Clumps are allowed to settle and the cellsare decanted into a clean tube, care being taken to avoid includingconnective tissue, in order to minimize fibroblast growth. The sample isirradiated at 4500 R. Cells are washed once with serum-free medium,placed into 96-well plates [one spleen/10 plates (approximately 2-5×10⁵cells/well) and peritoneal exudate cell suspension (PECS) (<3×10³cells/well) in a total volume of 100 μl/well] and incubated at 37° C.until ready to be used. They can also be stored in sterile tubeovernight at 4° C.

Example 11 Screening Potential Modulators of P450RAI-2

Antisense nucleic acids or oligonucleotides (RNA or preferably DNA) thatinhibit cellular RA-induced P450RAI-2 production can be used to inhibitmetabolism of RA by P450RAI-2 [Monia, 1996]. Antisense oligonucleotides,typically 15 to 20 bases long, bind to the sense mRNA or pre mRNA regioncoding for the protein of interest, which can inhibit translation of thebound mRNA to protein. The cDNA sequence encoding human P450RAI-2 canthus be used to design a series of oligonucleotides which together spana large portion, or even the entire cDNA sequence. Theseoligonucleotides can be tested to determine which provides the greatestinhibitory effect on the expression of the protein [Stewart, 1996]. Thiscan be done by exposing cells to the various oligonucleotides andmeasuring subsequent changes in human P450RAI-2 activity or by usingantibodies to screen for inhibition of P450RAI-2 synthesis. The mostsuitable mRNA target sites include 5′- and 3′-untranslated regions aswell as the initiation codon. Other regions might be found to be more orless effective. Alternatively, an antisense nucleic acid oroligonucleotide may bind to P450RAI-2 DNA coding or regulatorysequences.

Rather than reducing RA metabolism by inhibiting P450RAI-2 geneexpression at the nucleic acid level, activity of the P450RAI-2 proteinmay be directly inhibited by binding to an agent, such as, for example,a suitable small molecule or a monoclonal antibody.

The present invention thus includes a method of screening drugs fortheir effect on activity (i.e., as a modulator, preferably an inhibitor)of a retinoic acid inducible protein. The method includes exposing theprotein to a prospective inhibitor (or modulating) drug and determiningthe effect on protein activity. The measured activity might behydroxylation of a retinoid, particularly all-trans retinoic acid, orhydroxylation of a retinoic acid, particularly all-trans retinoic acid,at the 4 position of the β-ionone ring thereof. For screening drugs foruse in humans, P450RAI-2 itself is particularly useful for testing theeffectiveness of such drugs. Prospective drugs could also be tested forinhibition of the activity of other P450 cytochromes, which are desirednot to be inhibited. In this way, drugs which selectively inhibitP450RAI-2 over other P450s could be identified.

Another system for screening for potential modulators, preferablyinhibitors, of a P450RAI-2 protein includes a stably transfected cellline having incorporated therein DNA of a reporter gene (e.g.,β-galactosidase, firefly luciferase, or the like) and of the P450RAI-2,in which expression of both genes is inducible by exposure of the cellsto RA. Expression of the reporter gene provides a measure of theinduction of the expression system and therefore provides an indicationof the amount of RA present. Exposure of the cells to RA leads to RAmetabolism and, with time, such metabolism leads to a decrease in thedegree of induction which is indicated by the reporter protein. Exposureof the cells to RA in the presence of an agent that inhibits P450RAI-2metabolism of RA results in decreased RA metabolism, whereas exposure ofthe cells to RA in the presence of an agent that does not inhibitP450RAI-2 metabolism of RA has no effect on RA metabolism. A comparisonof expression of the reporter gene in the presence of RA alone and inthe presence of both RA and a potential inhibitory drug thus gives ameasure of the effectiveness of the drug in inhibiting metabolism of RAby the P450RAI-2 protein.

One system for screening for potential inhibitors of a P450RAI-2 proteinincludes a cell line in which the endogenous P450RAI-2 gene is notpresent or not functional or not expressed. In this cell line, acytochrome P450RAI-2 expression vector and an RA-inducible reporter geneare incorporated such that exposure of the cell line to RA results inmetabolism of RA by the expressed P450RAI-2 protein and a degree ofinduction of the reporter gene based on remaining active RA. Theaddition of an inhibitor of P450RAI-2 will decrease the rate ofmetabolism/degradation of RA and therefore increase theactivation/induction of the RA sensitive reporter gene.

Another system for screening of potential inhibitors (or othermodulators) using the same cell line would be to add radioactivesubstrate to the cells along with the potential inhibitors (ormodulators). Addition of the radioactive substrate, which could beall-trans retinoic acid, causes the production of radioactivemetabolites. Using a phase extraction procedure, such as that describedherein, the amount of these metabolites can be measured. The addition ofan inhibitor will cause a decrease in the generation of the radioactivemetabolites, which can be measured using β-scintillation counting orHPLC.

The invention thus provides a system for screening potential inhibitorsof RA catabolism by a P450RAI-2 protein. The system includes atransfected cell line having incorporated therein DNA of a reportergene, for example the luciferase gene exemplified above, in whichexpression of the reporter gene is inducible by exposure of the cells toRA. In this system, the P450RAI-2 gene is omitted, that is the reportergene is under the control of the native promoter for the P450RAI-2 gene.Expression of the reporter gene provides a measure of the induction ofthe expression system and therefore provides an indication of the amountof mRNA produced in response to exposure of the cells to RA. Exposure ofthe cells to RA in the presence of an agent that inhibits induction ofthe expression system indicates that the agent is a potential inhibitorof RA catabolism, i.e., provides a measure of the effectiveness of theagent as a drug in inhibiting the expression of P450RAI-2 gene and thusmetabolism of RA.

There is the possibility that cellular retinoic acid-binding protein(CRABP) [Adamson, 1993] is involved in binding of a retinoid substrateto a P450RAI-2 protein of the present invention. The effect of thepresence of CRABP, derivatives, synthetic fragments or analogs thereofcould thus be determined according to screening methods of the presentinvention; effectiveness of such agents in enhancing RA metabolism canalso be determined.

The present invention allows the skilled artisan to prepare bispecificantibodies and tetrameric antibody complexes. Bispecific antibodies canbe prepared by forming hybrid hybridomas [Staerz, 1986a & b].

The present invention includes three types of compounds related toretinoids: those that inhibit enzymatic activity of P450RAI-2, therebyinhibiting metabolism of RA; those retinoids that evade metabolism byP450RAI-2; and those compounds that repress induction of P450RAI-2 geneexpression.

Compositions of the invention are administered to subjects in abiologically compatible form suitable for pharmaceutical administrationin vivo. By “biologically compatible from suitable for administration invivo” is meant a form of the composition to be administered in which anytoxic effects are outweighed by the therapeutic effects of thecomposition. The term “subject” is intended to include living organismsin which a desired therapeutic response can be elicited, e.g. mammals.Examples of subjects include human, dogs, cats, mice, rats andtransgenic species thereof. Administration of a therapeutically activeamount of the therapeutic compositions of the present invention isdefined as an amount effective, at dosages and for periods of timenecessary to achieve the desired result. For example, a therapeuticallyactive amount of a compound that inhibits catabolism of RA by aP450RAI-2 protein may vary according to factors such as the diseasestate, age, sex, and weight of the individual, as well as target tissueand mode of delivery. Dosage regimes may be adjusted to provide theoptimum therapeutic response. For example, several divided doses may beadministered daily or the dose may be proportionally reduced asindicated by the exigencies of the therapeutic situation.

Compounds of the present invention, such as those that are found toinhibit metabolism of RA by P450RAI-2 enzymes and that are useful asanticancer agents and in the treatment, amelioration, or prevention ofskin disorders for which retinoic acid is useful, for example, may beused topically. In this regard they may be included in compositions fortherapy in animals, including humans, for premalignant epithelial celllesions, as a prophylaxis against tumor promotion in epithelial cellsand treatment for dermatoses such as ichthyoses, follicular disorders,benign epithelial disorders, and other proliferative skin diseases, suchas acne, psoriasis, eczema, atopic dermatitis, nonspecific dermatitisand the like.

Topical compositions are usually formulated with a pharmaceuticallyacceptable carrier in liquid, semi-solid or solid form. Apharmaceutically acceptable carrier is a material that is nontoxic andgenerally inert and does not affect the functionality of the activeingredients adversely. Such materials are well known and include thosematerials sometimes referred to as diluents or vehicles (excipients) inthe pharmaceutical formulation art. The carrier may be organic orinorganic in nature. Examples of pharmaceutically acceptable carriersare water, gelatin, lactose, starch, mineral oil, cocoa butter,dextrose, sucrose, sorbitol, mannitol, gum, acacia, alginates,cellulose, talc, magnesium stearate, polyoxyethylene sorbitanmonolaurate, and other commonly used pharmaceutical carriers. Inaddition to an active ingredient and carrier, the formulation maycontain minor amounts of additives such as flavoring agents, coloringagents, thickening or gelling agents, emulsifiers, wetting agents,buffers, stabilizers, and preservatives such as antioxidants.

Certain compositions may be administered enterally. For oraladministration, suitable forms are, for example, tablets, pills, syrups,suspensions, emulsions, solutions, powders and granules.

As anti-tumor agents or as part of an anti-tumor formulation, forexample, compounds of the present invention can be used in a similarmanner to retinoids used for treating various tumours, such as all-transretinoic acid. The dose to be administered, whether a single dose,multiple does or daily dose, will of course vary with the particularcompound employed because of the varying potency of the activeingredient, the chosen route of administration, the size of therecipient, the type of tumor, and the nature of the patient's condition.The dosage to be administered is not subject to definite bounds, but itwill usually be an effective amount, or the equivalent on a molar basisof the pharmacologically active free form produced from a dosageformulation upon the metabolic release of the active drug to achieve itsdesired pharmacological and physiological effects. An oncologist skilledin the art of cancer treatment will be able to ascertain without undueexperimentation, appropriate protocols for the effective administrationof the compounds of this present invention.

Nucleic acids which encode proteins having biological activity of aP450RAI-2 protein can be used to generate either transgenic animals or“knock out” animals which, in turn, are useful in the development andscreening of therapeutically useful reagents. A transgenic animal (e.g.,a mouse) is an animal having cells that contain a transgene, whichtransgene was introduced into the animal or an ancestor of the animal ata prenatal, e.g., an embryonic stage. A transgene is a DNA which isintegrated into the genome of a cell from which a transgenic animaldevelops. In one embodiment, a human P450RAI-2 cDNA, comprising thenucleotide sequence shown in SEQ ID NO:4, or an appropriate variant orsubsequence thereof, can be used to generate transgenic animals thatcontain cells which express human P450RAI-2 protein. Methods forgenerating transgenic animals, particularly animals such as mice, havebecome conventional in the art are described, for example, in U.S. Pat.Nos. 4,736,866 and 4,870,009. In a preferred embodiment, plasmidscontaining recombinant molecules of the invention are microinjected intomouse embryos. In particular, the plasmids are microinjected into themale pronuclei of fertilized one-cell mouse eggs; the injected eggs aretransferred to pseudo-pregnant foster females; and, the eggs in thefoster females are allowed to develop to term. [Hogan, 1986].Alternatively, an embryonal stem cell line can be transfected with anexpression vector comprising nucleic acid encoding a protein havingP450RAI-2 activity, and cells containing the nucleic acid can be used toform aggregation chimeras with embryos from a suitable recipient mousestrain. The chimeric embryos can then be implanted into a suitablepseudopregnant female mouse of the appropriate strain and the embryobrought to term. Progeny harboring the transfected DNA in their germcells can be used to breed uniformly transgenic mice.

Typically, particular cells would be targeted for P450RAI-2 transgeneincorporation by use of tissue specific enhancers operatively linked tothe P450RAI-2 encoding gene. For example, promoters and/or enhancerswhich direct expression of a gene to which they are operatively linkedpreferentially in cardiac muscle cells can be used to create atransgenic animal which expresses a P450RAI-2 protein preferentially incardiac muscle tissue. Examples of suitable promoters and enhancersinclude those which regulate the expression of the genes for cardiacmyosin and cardiac actin. Transgenic animals that include a copy of anP450RAI-2 transgene introduced into the germ line of the animal at anembryonic stage can also be used to examine the effect of increasedP450RAI-2 expression in various tissues.

The pattern and extent of expression of a recombinant molecule of theinvention in a transgenic mouse is facilitated by fusing a reporter geneto the recombinant molecule such that both genes are co-transcribed toform a polycistronic mRNA. The reporter gene can be introduced into therecombinant molecule using conventional methods such as those describedin Sambrook et al., [Sambrook,1989]. Efficient expression of bothcistrons of the polycistronic mRNA encoding the protein of the inventionand the reporter protein can be achieved by inclusion of a knowninternal translational initiation sequence such as that present inpoliovirus mRNA. The reporter gene should be under the control of theregulatory sequence of the recombinant molecule of the invention and thepattern and extent of expression of the gene encoding a protein of theinvention can accordingly be determined by assaying for the phenotype ofthe reporter gene. Preferably the reporter gene codes for a phenotypenot displayed by the host cell and the phenotype can be assayedquantitatively. Examples of suitable reporter genes include lacZ($-galactosidase), neo (neomycin phosphotransferase), CAT(chloramphenicol acetyltransferase) dhfr (dihydrofolate reductase),aphIV (hygromycin phosphotransferase), lux (luciferase), uidA($-glucuronidase). Preferably, the reporter gene is lacZ which codes for$-galactosidase. $-galactosidase can be assayed using the lactoseanalogue X-gal (5-bromo-4-chloro-3-indolyl-b-D-galactopyranoside) whichis broken down by $-galactosidase to a product that is blue in color[Old].

Although experimental animals used in the preferred embodiment disclosedare mice, the invention should not be limited thereto. It can bedesirable to use other species such as, for example, rats, hamsters,rabbits and sheep.

The transgenic animals of the invention can be used to investigate themolecular basis of RA metabolism. The transgenic animals of theinvention can also be used to test substances for the ability toprevent, slow or enhance RA metabolism. A transgenic animal can betreated with the substance in parallel with an untreated controltransgenic animal.

Cells from the transgenic animals of the invention can be cultured usingstandard tissue culture techniques. In particular, cells carrying therecombinant molecule of the invention can be cultured and used to testsubstances for the ability to prevent, slow or enhance RA metabolism.

Additionally, the non-human homologs of genes encoding proteins havingP450RAI-2 activity can be used to construct a “knock out” animal whichhas a defective or altered P450RAI-2 gene. For example, with establishedtechniques, a portion of murine genomic P450RAI-2 DNA (e.g., an exon),can be deleted or replaced with another gene, such as a gene encoding aselectable marker which can be used to monitor integration. The alteredP450RAI-2 DNA can then be transfected into an embryonal stem cell line.The altered P450RAI-2 DNA will homologously recombine with theendogenous P450RAI-2 gene in certain cells and clones containing thealtered gene can be selected. Cells containing the altered gene areinjected into a blastocyst of an animal, such as a mouse, to formaggregation chimeras as described for transgenic animals. Chimericembryos are implanted as described above. Transmission of the alteredgene into the germline of a resultant animal can be confirmed usingstandard techniques and the animal can be used to breed animals havingan altered P450RAI-2 gene in every cell [Lemoine, 1996]. Accordingly, aknockout animal can be made which cannot express a functional P450RAI-2protein. Such a knockout animal can be used, for example, to test theeffectiveness of an agent in the absence of a P450RAI-2 protein.

The antisense nucleic acids and oligonucleotides of the invention areuseful for inhibiting expression of nucleic acids (e.g. mRNAs) encodingproteins having P450RAI-2 activity. Since proteins having P450RAI-2activity are associated with metabolism of agents which can act on thecell, e.g., RA, decreasing expression of such proteins can increasesensitivity of the cell to such agents. Antisense nucleic acids can beintroduced into a drug resistant cell in culture to inhibit P450RAI-2expression. One or more antisense nucleic acids, such asoligonucleotides, can be added to cells in culture media, typically, forexample, at 200 μg/ml.

The antisense nucleic acids of the invention, or oligonucleotidesthereof, can thus be used in gene therapy to correct or prevent retinoicacid or other retinoid resistance in a subject. For example, antisensesequences can be used to render retinoic acid or other retinoidresistant malignant cells sensitive to chemotherapeutic agents.Administration of antisense nucleic acids to a subject may be mosteffective when the antisense nucleic acid is contained in a recombinantexpression vector which allows for continuous production of antisenseRNA. Recombinant molecules comprising an antisense nucleic acid oroligonucleotide thereof, can be directly introduced into tissues,including lung tissue in vivo, using delivery vehicles such asliposomes, retroviral vectors, adenoviral vectors and DNA virus vectors.A delivery vehicle can be chosen which can be targeted to a cell ofinterest in the subject (e.g. a retinoid resistant tumor cell).Antisense nucleic acids can also be introduced into isolated cells, suchas those of the haematopoietic system, ex vivo using viral vectors orphysical techniques such as microinjection and electroporation orchemical methods such as coprecipitation and incorporation of DNA intoliposomes, and such cells can be returned to the donor. Recombinantmolecules can be delivered in the form of an aerosol or by lavage.

Accordingly, the invention provides a method for inhibiting retinoicacid or other retinoid resistance of a resistant cell by introducinginto the resistant cell a nucleic acid which is antisense to a nucleicacid which encodes the protein identified as SEQ ID NO:5.

The nucleic acids of the invention can further be used to designribozymes which are capable of cleaving a single-stranded nucleic acidencoding a protein having P450RAI-2 activity, such as an mRNA. Acatalytic RNA (ribozyme) having ribonuclease activity can be designedwhich has specificity for a P450RAI-2-encoding mRNA based upon thesequence of a nucleic acid of the invention. For example, a derivativeof a Tetrahymena L-19IVS RNA can be constructed in which the basesequence of the active site is complementary to the base sequence to becleaved in a P450RAI-2-encoding mRNA. [Cech a and b]. Alternatively, anucleic acid of the invention could be used to select a catalytic RNAhaving a specific ribonuclease activity from a pool of RNA molecules[Bartel, 1993].

The isolated nucleic acids and antisense nucleic acids of the inventioncan be used to construct recombinant expression vectors as describedpreviously. These recombinant expression vectors are then useful formaking transformant host cells containing the recombinant expressionvectors, for expressing protein encoded by the nucleic acids of theinvention, and for isolating proteins of the invention as describedpreviously. The isolated nucleic acids and antisense nucleic acids ofthe invention can also be used to construct transgenic and knockoutanimals as described previously.

The isolated proteins of the invention are useful for making antibodiesreactive against proteins having P450RAI-2 activity, as describedpreviously. Alternatively, the antibodies of the invention can be usedto isolate a protein of the invention by standard immunoaffinitytechniques. Furthermore, the antibodies of the invention, includingbispecific antibodies are useful for diagnostic purposes.

Molecules which bind to a protein comprising an amino acid sequenceshown in SEQ ID NO:5 can also be used in a method for killing a cellwhich expresses the protein, wherein the cell takes up the molecule.Preferably, the cell is a tumor cell. Destruction of such cells can beaccomplished by labeling the molecule with a substance having toxic ortherapeutic activity. The term “substance having toxic or therapeuticactivity” as used herein is intended to include molecules whose actioncan destroy a cell, such as a radioactive isotope, a toxin (e.g.diphtheria toxin or ricin), or a chemotherapeutic drug, as well as cellswhose action can destroy a cell, such as a cytotoxic cell. The moleculebinding to the P450RAI-2 can be directly coupled to a substance having atoxic or therapeutic activity or may be indirectly linked to thesubstance. In one example, the toxicity of the molecule taken up by thecell is activated by P450RAI-2 protein.

The invention also provides a diagnostic kit for identifying tumor cellscomprising a molecule which binds to a protein comprising an amino acidsequence shown in SEQ ID NO:5, for example, for incubation with a sampleof tumor cells; means for detecting the molecule bound to the protein,unreacted protein or unbound molecule; means for determining the amountof protein in the sample; and means for comparing the amount of proteinin the sample with a standard. Preferably, the molecule is a monoclonalantibody. In some embodiments of the invention, the detectability of themolecule which binds to P450RAI-2 is activated by said binding (e.g.,change in fluorescence spectrum, loss of radioisotopic label). Thediagnostic kit can also contain an instruction manual for use of thekit.

The invention further provides a diagnostic kit for identifying tumorcells comprising a nucleotide probe complementary to the sequence, or anoligonucleotide fragment thereof, shown in SEQ ID NO:4, for example, forhybridization with mRNA from a sample of tumor cells; means fordetecting the nucleotide probe bound to mRNA in the sample with astandard. The diagnostic kit can also contain an instruction manual foruse of the kit.

Discussion of Results

The present inventors have have identified a novel retinoic acidmetabolizing cytochrome P450. Consequently, at least two genes, encodingall-trans-RA metabolizing enzymes P450RAI-1 [White, J. A., et al.(1997), White, J., et al. (1998)] and P450RAI-2 are expressed in humans.The predicted amino acid sequences of these enzymes (P450RAI-1 andP450RAI-2) are 42% similar overall. Regions corresponding to functionaldomains such as those for heme binding and putative substrate bindingexhibit the highest degrees of similarity. P450RAI-1 and -2 are alsoconserved across species from zebrafish to humans suggesting that theseenzymes may be functionally distinct [White, J. A., et al. (1997),Nelson, D. (1999); White, J. A. et al. (1996)]. The genomic structuresof these two genes are quite distinct-, P450RAI-1 is comprised of 7exons while P450RAI-2 has 6 and there is no clear evidence of conservedintron/exon boundaries between the two genes [White, J., et al. (1998);Nelson, D. (1999)], These data support the possibility that these genesdiverged from a common ancestral gene prior to the emergence of mammals.

P450RAI-2 can metabolize all-trans-RA with efficiency comparable to thatof P450RAI-1. HPLC analysis comparing these enzymes reveals theirstriking similarities with respect to conversion of all-trans-RA into4-OH- and 4-oxo RA and characteristic secondary products. Moreover,P450RAI-1 and P450RAI-2 share surprisingly similar specificities forretinoids as determined by our competition studies. The all-transmetabolite of RA is clearly the preferred substrate for both enzymeswith a rank-order of: all-trans-RA>9 cis RA>13 cis. Other retinoids suchas retinol and retinaldehyde are very poor competitors suggesting thatthey are unlikely to be natural substrates for these enzymes undernormal physiological conditions. This is in contrast to a recent reportsuggesting that P450RAI (CYP26A) may be involved in the activation stepof retinol [Lane, M., et al. (1999)]. These similarities would suggestthat, at least with respect to metabolic activity, these enzymes may beequivalent. Although this is somewhat surprising given their differencesin sequence, there are many RA binding proteins—RARs, RXRs, CRABPs—whichare widely different in primary amino acid sequences. It is possiblethat the differences in sequence reflect differences in the abilities ofthese enzymes to interact with other proteins such as CRABPs which havebeen proposed to modify all-transRA metabolic activities in cells[Boylan, J. & Gudas, L. (1992); Napoli, J. (1996)].

Although the enzymatic activities of P450RAI-1 and -2 may be similar, itappears that their tissue specific expression is not. Tissue dot blotand northern blot analyses indicate that in the adult, P450RAI-2 isbroadly expressed at low levels in most tissues but is predominantlyexpressed in brain tissues, notably pons and cerebellum. P450RAI-1, onthe other hand, does not show appreciable expression in any of the humanbrain tissues evaluated. During development numerous studies haveindicated that the role of P450RAI-1 is to regulate local levels ofall-trans-RA and restrict certain tissues from all-trans-RA activity.Developing retina exhibit an exquisite pattern of coordinated expressionof P450RAI-1, and the all-trans-RA synthesizing enzymes RALDH-2 andALDH-1 [McCafferty et al., (1999)]. Given that the EST corresponding toP450RAI-2 (accession # AA012833) was derived from an adult retinallibrary suggests that this enzyme may also play a role in the balance ofall-trans-RA in retinal tissue.

Expression of P450RAI-2 in adult human brain suggests that all-trans-RAmay play an important homeostatic role in brain tissue. In this regard,it has recently been shown that all-trans-RA signaling pathways may beimportant for memory and learning since RARP/RXR(X knockout mice haveimpaired long-term potentiation and limited ability to negotiate awater-maze [Chiang, M. Y., (1998)]. If all trans-RA signaling pathwaysare involved in maintenance of higher order brain function then theregulation and function of enzymes like P450RAI-2 will be importantregulators of these pathways. The high level of expression of P450RAI-2in adult cerebellum suggests that it is protecting this tissue fromexposure to RA. Of note, developing cerebellum is highly sensitive tothe teratogenic effects of RA [Lammer, E. J., (1985); Lammer, E. &Armstrong, D. (1992)]. Also, Yamamoto et al. [Yamamoto, M., et al.(1998)], have reported evidence that RA may be synthesized from retinolin the choroid plexus of developing cerebellum, and that RA injectedinto the cerebellum is rapidly metabolized. These findings support thenotion of an important role for RA metabolism in cerebellum duringdevelopment which may also extend into adulthood. It is likely that thismetabolism is mediated by P450RAI-2.

Studies of several cell lines in culture indicate that P450RAI-2expression, similar to that of P450RAI-1, is regulated by all-trans-RA.For example, the induction by all-trans-RA of P450RAI-2 expression inthe breast epithelial adenocarcinoma cell line MCF-7 is comparable tothat of P450RAI-1. Interestingly, the transcriptional elements requiredfor RA-induction of P450RAI-2 may be different from those for inductionof P450RAI-1-, inspection of genomic sequence immediately upstream ofthe first exon of P450RAI-2 has not revealed any elements previouslydemonstrated to mediate a retinoid induction of transcription, whereaswe have identified a functional, conserved, canonical RA responseelement (RARE) within the first 200 bp of the P450RAI-1 promoter (M.P.;unpublished). Comparative studies of induction of these two genes at thetranscriptional level will help to discriminate possible similarities intheir regulation.

RA metabolism may be implicated in certain disease states such asdermatological conditions angiogenesis, immunological disorders, andcancer. The present work suggests that certain brain functions may alsodepend on normal retinoid metabolism. There is interest in inhibitingthis activity to increase the cell sensitivity to the differentiating orapoptotic affects of all-trans-RA; recent clinical trials withall-trans-RA metabolism inhibitors suggest that this may be a viableapproach to treat diseases which respond positively to retinoids. Theidentification of a second P450RAI provides another potentially usefultarget for rational drug design.

While the present invention has been described with reference to whatare presently considered to be the preferred examples, it is to beunderstood that the invention is not limited to the disclosed examples.To the contrary, the invention is intended to cover variousmodifications and equivalent arrangements included within the spirit andscope of the appended claims.

All publications, patents and patent applications are hereinincorporated by reference in their entirety to the same extent as ifeach individual publication, patent or patent application wasspecifically and individually indicated to be incorporated by referencein its entirey.

REFERENCES

Particulars of references cited above are given below. All of the listedreferences are incorporated herein by reference.

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1. An isolated nucleic acid molecule selected from the group consistingof (a) a nucleic acid molecule comprising the nucleotide sequence of SEQID NO:4, wherein T can be T or U, (b) a nucleic acid molecule comprisinga nucleotide sequence perfectly complementary to (a), and (c) a nucleicacid molecule comprising a nucleotide sequence degenerate to (a) or (b).2. An isolated nucleic acid molecule encoding an amino acid sequence atleast 95% identical to the full length of SEQ ID NO: 5, wherein saidnucleic acid encodes a protein capable of oxidizing a retinoid, and saidnucleic acid is not SEQ ID NO: 2 or
 3. 3. The nucleic acid molecule ofclaim 2 that is a fragment of SEQ ID NO: 2 or 3, said fragment encodingan amino acid sequence that is at least 95% identical to the full lengthof SEQ ID NO: 5 and is capable of oxidizing a retinoid.
 4. The isolatednucleic acid of claim 1, wherein the nucleic acid molecule comprises SEQID NO:
 28. 5. The isolated nucleic acid molecule of claim 1 wherein thenucleic acid molecule encodes a protein that oxidizes a retinoid at the4-position of the β-ionone ring.
 6. The isolated nucleic acid moleculeof claim 5, wherein the nucleic acid encodes a protein that hydroxylatesa retinoid at the 4-position of the β-ionone ring.
 7. The isolatednucleic acid molecule of claim 6 wherein said retinoid is a retinoicacid.
 8. A vector comprising the nucleic acid molecule of claim
 1. 9. Avector comprising the nucleic acid molecule of claim
 2. 10. The isolatedhost cell transformed with a vector of claim
 8. 11. An isolated hostcell transformed with the vector of claim
 9. 12. A stably transfectedcell line which expresses a protein encoded by the nucleic acid moleculeof claim
 1. 13. An isolated culture of cells transformed with arecombinant DNA molecule comprising the nucleic acid molecule accordingto claim
 1. 14. The isolated culture of cells according to claim 13,wherein the cells are eukaryotic.
 15. A process for producing anall-trans retinoic acid metabolizing cytochrome P450 polypeptide,P450RAI-2 protein, the process comprising the steps of: (i) preparing aDNA fragment including the nucleic acid molecule according to claim 1which encodes said protein; (ii) incorporating the DNA fragment into anexpression vector to obtain a recombinant DNA molecule which includesthe DNA fragment and is capable of undergoing replication; (iii)transforming an isolated host cell with said recombinant DNA molecule toproduce a transformant which can express said protein; (iv) culturingthe transformant to produce said protein; and (v) recovering saidprotein from resulting cultured mixture.
 16. A method of using thestably transfected cell line of claim 12 to determine the effect of adrug on the activity of a protein of SEQ ID NO: 5, comprising: (i)exposing the stably transfected cell line of claim 12 expressing theprotein to a drug; and (ii) determining the effect of the drug on theactivity of the protein.
 17. The method of claim 16, comprising exposingthe cell line to a substrate of the protein, under conditions in whichsaid protein is expressed in an active form, so as to expose the proteinto the substrate.
 18. The method of claim 16, wherein said activity iscatalyzing oxidation of a substrate, and (ii) comprises detecting theoxidized substrate.
 19. The method of claim 18, further comprisingexposing the cell line to the substrate.
 20. The method of claim 19,wherein the substrate is a retinoid.
 21. The method of claim 20, whereinthe retinoid is a retinoic acid.
 22. The method of claim 21, wherein theretinoic acid is all-trans retinoic acid.
 23. The method of claim 18,wherein said activity is oxidation of the β-ionone ring of thesubstrate.
 24. The method of claim 23, wherein said oxidation ishydroxylation.
 25. The method of claim 16, wherein said stablytransfected cell line comprises the nucleic acid molecule of SEQ ID NO:4.
 26. The method of claim 16, further comprising (a) exposing a secondcell line expressing a second protein to the drug, wherein the secondcell line is separate from the stably transfected cell line and thesecond protein is a cytochrome P450, and (b) determining the effect ofthe drug on the activity of the protein of SEQ ID NO: 5 relative to theeffect of the drug on the activity of the second protein.
 27. The methodof claim 26, wherein the activity of the protein of SEQ ID NO: 5 iscatalyzing oxidation of a first substrate, and the activity of thesecond protein is catalyzing oxidation of a second substrate, and (b)comprises detecting the amounts of oxidized first substrate and oxidizedsecond substrate.
 28. The method of claim 26, comprising exposing thestably transfected cell line to a first substrate in the presence of thedrug and exposing the second line to a second substrate in the presenceof the drug.
 29. The method of claim 28, wherein the first and secondsubstrate are the same.
 30. The method of claim 28 wherein the substrateis a retinoid, or wherein the substrate is a retinoic acid, or isall-trans retinoic acid.
 31. The method of claim 27, wherein saidactivity is the ability to oxidize a retinoid at the 4-position of theβ-ionone ring.
 32. The method of claim 31, wherein said activity is theability to hydroxylate a retinoid at the 4-position of the β-iononering.
 33. The method of claim 30, wherein said retinoid is a retinoicacid.
 34. The method of claim 33, wherein said retinoic acid isall-trans retinoic acid.
 35. The method of claim 26, wherein said secondprotein is selected from the group of proteins encoded by: (a) anucleotide sequence that hybridizes under high stringency conditions,wherein high stringency conditions include a wash step of about 0.2×SSCat 50° C., to the nucleotide sequence shown as SEQ ID NO:13 or SEQ IDNO:14, and encodes a protein that oxidizes a retinoid; and (b) anucleotide sequence that hybridizes under high stringency conditions,wherein high stringency conditions include a wash step of about 0.2×SSCat 50° C., to the nucleotide sequence shown as SEQ ID NO:13 or SEQ IDNO:14, and encodes a protein that hydroxylates retinoic acid at the 4position of the β-ionone ring.
 36. The method of claim 35, wherein saidsecond protein is a human protein.
 37. The method of claim 36, whereinsaid second protein comprises the amino acid sequence encoded by thenucleotide sequence identified as SEQ ID NO:13.
 38. The method of claim30, comprising exposing the stably transfected cell line to variousconcentrations of said retinoid.
 39. The method of claim 30, comprisingexposing the second cell line to various concentrations of saidretinoid.